@article{RuzanskiSmirnovaRejzeketal.2013,
  author    = {Ruzanski, Christian and Smirnova, Julia and Rejzek, Martin and Cockburn, Darrell and Pedersen, Henriette L. and Pike, Marilyn and Willats, William G. T. and Svensson, Birte and Steup, Martin and Ebenh{\"o}h, Oliver and Smith, Alison M. and Field, Robert A.},
  title     = {A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night},
  series = {The journal of biological chemistry},
  volume    = {288},
  journal   = {The journal of biological chemistry},
  number    = {40},
  publisher = {American Society for Biochemistry and Molecular Biology},
  address   = {Bethesda},
  issn      = {0021-9258},
  doi       = {10.1074/jbc.M113.497867},
  pages     = {28581 -- 28598},
  year      = {2013},
  abstract  = {Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a glucosyl buffer to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway.},
  language  = {en}
}
@article{ComparotMossKoettingStettleretal.2010,
  author    = {Comparot-Moss, Sylviane and Koetting, Oliver and Stettler, Michaela and Edner, Christoph and Graf, Alexander and Weise, Sean E. and Streb, Sebastian and Lue, Wei-Ling and MacLean, Daniel and Mahlow, Sebastian and Ritte, Gerhard and Steup, Martin and Chen, Jychian and Zeeman, Samuel C. and Smith, Alison M.},
  title     = {A putative phosphatase, LSF1, is required for normal starch turnover in Arabidopsis leaves},
  issn      = {0032-0889},
  doi       = {10.1104/pp.109.148981},
  year      = {2010},
  abstract  = {A putative phosphatase, LSF1 (for LIKE SEX4; previously PTPKIS2), is closely related in sequence and structure to STARCH-EXCESS4 (SEX4), an enzyme necessary for the removal of phosphate groups from starch polymers during starch degradation in Arabidopsis (Arabidopsis thaliana) leaves at night. We show that LSF1 is also required for starch degradation: lsf1 mutants, like sex4 mutants, have substantially more starch in their leaves than wild-type plants throughout the diurnal cycle. LSF1 is chloroplastic and is located on the surface of starch granules. lsf1 and sex4 mutants show similar, extensive changes relative to wild-type plants in the expression of sugar-sensitive genes. However, although LSF1 and SEX4 are probably both involved in the early stages of starch degradation, we show that LSF1 neither catalyzes the same reaction as SEX4 nor mediates a sequential step in the pathway. Evidence includes the contents and metabolism of phosphorylated glucans in the single mutants. The sex4 mutant accumulates soluble phospho- oligosaccharides undetectable in wild-type plants and is deficient in a starch granule-dephosphorylating activity present in wild-type plants. The lsf1 mutant displays neither of these phenotypes. The phenotype of the lsf1/sex4 double mutant also differs from that of both single mutants in several respects. We discuss the possible role of the LSF1 protein in starch degradation.},
  language  = {en}
}
@article{SonnewaldBasnerGreveetal.1995,
  author    = {Sonnewald, Uwe and Basner, Astrid and Greve, Burkhard and Steup, Martin},
  title     = {A second L-type isozyme of potato glucan phosphorylase : cloning, antisense inhibition and expression analysis},
  year      = {1995},
  language  = {en}
}
@article{FettkeChiaEckermannetal.2006,
  author    = {Fettke, J{\"o}rg and Chia, Tansy and Eckermann, Nora and Smith, Alison M. and Steup, Martin},
  title     = {A transglucosidase necessary for starch degradation and maltose metabolism in leaves at night acts on cytosolic heteroglycans (SHG)},
  issn      = {0960-7412},
  doi       = {10.1111/j.1365-313X.2006.02732.x},
  year      = {2006},
  abstract  = {The recently characterized cytosolic transglucosidase DPE2 (EC 2.4.1.25) is essential for the cytosolic metabolism of maltose, an intermediate on the pathway by which starch is converted to sucrose at night. In in vitro assays, the enzyme utilizes glycogen as a glucosyl acceptor but the in vivo acceptor molecules remained unknown. In this communication we present evidence that DPE2 acts on the recently identified cytosolic water-soluble heteroglycans (SHG) as does the cytosolic phosphorylase (EC 2.4.1.1) isoform. By using in vitro two-step C-14 labeling assays we demonstrate that the two transferases can utilize the same acceptor sites of the SHG. Cytosolic heteroglycans from a DPE2-deficient Arabidopsis mutant were characterized. Compared with the wild type the glucose content of the heteroglycans was increased. Most of the additional glucosyl residues were found in the outer chains of SHG that are released by an endo- alpha-arabinanase (EC 3.2.1.99). Additional starch-related mutants were characterized for further analysis of the increased glucosyl content. Based on these data, the cytosolic metabolism of starch-derived carbohydrates is discussed},
  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{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}
}
@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{StahlLinosKarasetal.1997,
  author    = {Stahl, Bernd and Linos, Alexandros and Karas, Michael and Hillenkamp, Franz and Steup, Martin},
  title     = {Analysis of fructans from higher plants by matrix-assisted laser desorption/ionization mass spectrometry},
  year      = {1997},
  language  = {en}
}
@article{KehrHaebelBlechschmidtSchneideretal.1999,
  author    = {Kehr, Julia and Haebel, Sophie and Blechschmidt-Schneider, Sabine and Willmitzer, Lothar and Steup, Martin and Fisahn, Joachim},
  title     = {Analysis of phloem protein patterns from different organs of Cucurbita maxima Duch. by matrix-assisted laser desorption/ionization time of flight mass spectroscopy combined with sodium dodecyl sufate-polyacryilamide gel electrophoresis},
  year      = {1999},
  language  = {en}
}
@article{DuwenigSteupWillmitzeretal.1997,
  author    = {Duwenig, Elke and Steup, Martin and Willmitzer, Lothar and Kossmann, Jens},
  title     = {Antisense inhibition of cytosolic phosphorylase in potato plants (Solanum tuberosum L.) affects tuber sprouting and flower formation with only little impact on carbohydrate metabolism},
  year      = {1997},
  language  = {en}
}
@article{ReimannRitteSteupetal.2002,
  author    = {Reimann, Rezarta and Ritte, Gerhard and Steup, Martin and Appenroth, Klaus-J.},
  title     = {Association of a-amylase and the R1 protein with starch granules precedes the initiation of net starch degradation in turions of Spirodela polyrhiza},
  issn      = {0031-9317},
  year      = {2002},
  language  = {en}
}
@article{MalinovaSteupFettke2013,
  author    = {Malinova, Irina and Steup, Martin and Fettke, J{\"o}rg},
  title     = {Carbon transitions from either Calvin cycle or transitory starch to heteroglycans as revealed by 14-C-labeling experiments using protoplasts from Arabidopsis},
  series = {Physiologia plantarum},
  volume    = {149},
  journal   = {Physiologia plantarum},
  number    = {1},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0031-9317},
  doi       = {10.1111/ppl.12033},
  pages     = {25 -- 44},
  year      = {2013},
  abstract  = {Plants metabolize transitory starch by precisely coordinated plastidial and cytosolic processes. The latter appear to include the action of water-soluble heteroglycans (SHG(in)) whose monosaccharide pattern is similar to that of apoplastic glycans (SHG(ex)) but, unlike SHG(ex), SHG(in) strongly interacts with glucosyl transferases. In this study, we analyzed starch metabolism using mesophyll protoplasts from wild-type plants and two knock-out mutants [deficient in the cytosolic transglucosidase, disproportionating isoenzyme 2 (DPE2) or the plastidial phosphoglucomutase (PGM1)] from Arabidopsis thaliana. Protoplasts prelabeled by photosynthetic (CO2)-C-14 fixation were transferred to an unlabeled medium and were darkened or illuminated. Carbon transitions from the Calvin cycle or from starch to both SHG(in) and SHG(ex) were analyzed. In illuminated protoplasts, starch turn-over was undetectable but darkened protoplasts continuously degraded starch. During illumination, neither the total C-14 content nor the labeling patterns of the sugar residues of SHG(in) were significantly altered but both the total amount and the labeling of the constituents of SHG(ex) increased with time. In darkened protoplasts, the C-14-content of most of the sugar residues of SHG(in) transiently and strongly increased and then declined. This effect was not observed in any SHG(ex) constituent. In darkened DPE2-deficient protoplasts, none of the SHG(in) constituents exhibited an essential transient increase in labeling. In contrast, some residues of SHG(in) from the PGM1 mutant exhibited a transient increase in label but this effect significantly differed from that of the wild type. Two conclusions are reached: first, SHG(in) and SHG(ex) exert different metabolic functions and second, SHG(in) is directly involved in starch degradation.},
  language  = {en}
}
@article{LiFranciscoZhouetal.2009,
  author    = {Li, Jing and Francisco, Perigio and Zhou, Wenxu and Edner, Christoph and Steup, Martin and Ritte, Gerhard and Bond, Charles S. and Smith, Steven M.},
  title     = {Catalytically-inactive beta-amylase BAM4 required for starch breakdown in Arabidopsis leaves is a starch- binding-protein},
  issn      = {0003-9861},
  doi       = {10.1016/j.abb.2009.07.024},
  year      = {2009},
  abstract  = {Of the four chloroplast beta-amylase (BAM) proteins identified in Arabidopsis, BAM3 and BAM4 were previously shown to play the major roles in leaf starch breakdown, although BAM4 apparently lacks key active site residues and beta- amylase activity. Here we tested multiple BAM4 proteins with different N-terminal sequences with a range of glucan substrates and assay methods, but detected no alpha-1,4-glucan hydrolase activity. BAM4 did not affect BAM1, BAM2 or BAM3 activity even when added in 10-fold excess, nor the BAM3-catalysed release of maltose from isolated starch granules in the presence of glucan water dikinase. However, BAM4 binds to amylopectin and to amylose-Sepharose whereas BAM2 has very low beta-amylase activity and poor glucan binding. The low activity of BAM2 may be explained by poor glucan binding but absence of BAM4 activity is not. These results suggest that BAM4 facilitates starch breakdown by a mechanism involving direct interaction with starch or other alpha-1,4-glucan.},
  language  = {en}
}
@article{GarzSandmannRadingetal.2012,
  author    = {Garz, Andreas and Sandmann, Michael and Rading, Michael and Ramm, Sascha and Menzel, Ralf and Steup, Martin},
  title     = {Cell-to-cell diversity in a synchronized chlamydomonas culture as revealed by single-cell analyses},
  series = {Biophysical journal},
  volume    = {103},
  journal   = {Biophysical journal},
  number    = {5},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2012.07.026},
  pages     = {1078 -- 1086},
  year      = {2012},
  abstract  = {In a synchronized photoautotrophic culture of Chlamydomonas reinhardtii, cell size, cell number, and the averaged starch content were determined throughout the light-dark cycle. For single-cell analyses, the relative cellular starch was quantified by measuring the second harmonic generation (SHG). In destained cells, amylopectin essentially represents the only biophotonic structure. As revealed by various validation procedures, SHG signal intensities are a reliable relative measure of the cellular starch content. During photosynthesis-driven starch biosynthesis, synchronized Chlamydomonas cells possess an unexpected cell-to-cell diversity both in size and starch content, but the starch-related heterogeneity largely exceeds that of size. The cellular volume, starch content, and amount of starch/cell volume obey lognormal distributions. Starch degradation was initiated by inhibiting the photosynthetic electron transport in illuminated cells or by darkening. Under both conditions, the averaged rate of starch degradation is almost constant, but it is higher in illuminated than in darkened cells. At the single-cell level, rates of starch degradation largely differ but are unrelated to the initial cellular starch content. A rate equation describing the cellular starch degradation},
  language  = {en}
}
@article{NeuhausThomSteupetal.1997,
  author    = {Neuhaus, Heinz Eckhard and Thom, E. and Steup, Martin and Kampfenkel, Karlheinz},
  title     = {Characterization of a novel eukaryotic ATP/ADP translocator located in the plastid envelope of Arabidopsis thaliana L.},
  year      = {1997},
  language  = {en}
}
@article{NakamuraOnoSawadaetal.2017,
  author    = {Nakamura, Yasunori and Ono, Masami and Sawada, Takayuki and Crofts, Naoko and Fujita, Naoko and Steup, Martin},
  title     = {Characterization of the functional interactions of plastidial starch phosphorylase and starch branching enzymes from rice endosperm during reserve starch biosynthesis},
  series = {Plant science : an international journal of experimental plant biology},
  volume    = {264},
  journal   = {Plant science : an international journal of experimental plant biology},
  publisher = {Elsevier},
  address   = {Clare},
  issn      = {0168-9452},
  doi       = {10.1016/j.plantsci.2017.09.002},
  pages     = {83 -- 95},
  year      = {2017},
  abstract  = {Functional interactions of plastidial phosphorylase (Phol) and starch branching enzymes (BEs) from the developing rice endosperm are the focus of this study. In the presence of both Phol and BE, the same branched primer molecule is elongated and further branched almost simultaneously even at very low glucan concentrations present in the purified enzyme preparations. By contrast, in the absence of any BE, glucans are not, to any significant extent, elongated by Phol. Based on our in vitro data, in the developing rice endosperm, Phol appears to be weakly associated with any of the BE isozymes. By using fluorophore-labeled malto-oligosaccharides, we identified maltose as the smallest possible primer for elongation by Phol. Linear dextrins act as carbohydrate substrates for BEs. By functionally interacting with a BE, Phol performs two essential functions during the initiation of starch biosynthesis in the rice endosperm: First, it elongates maltodextrins up to a degree of polymerization of at least 60. Second, by closely interacting with BEs, Phol is able to elongate branched glucans efficiently and thereby synthesizes branched carbohydrates essential for the initiation of amylopectin biosynthesis.},
  language  = {en}
}
@article{RitteEckermannHaebeletal.2000,
  author    = {Ritte, Gerhard and Eckermann, Nora and Haebel, Sophie and Lorberth, Ruth and Steup, Martin},
  title     = {Compartmentation of the starch-related R1 protein in higher plants},
  year      = {2000},
  language  = {en}
}
@article{FettkeMalinovaEckermannetal.2009,
  author    = {Fettke, J{\"o}rg and Malinova, Irina and Eckermann, Nora and Steup, Martin},
  title     = {Cytosolic heteroglycans in photoautotrophic and in heterotrophic plant cells},
  issn      = {0031-9422},
  doi       = {10.1016/j.phytochem.2009.03.016},
  year      = {2009},
  abstract  = {In plants several 'starch-related' enzymes exist as plastid- and cytosol-specific isoforms and in some cases the extraplastidial isoforms represent the majority of the enzyme activity. Due to the compartmentation of the plant cells, these extraplastidial isozymes have no access to the plastidial starch granules and, therefore, their in vivo function remained enigmatic. Recently, cytosolic heteroglycans have been identified that possess a complex pattern of the monomer composition and glycosidic bonds. The glycans act both as acceptors and donors for cytosolic glucosyl transferases. In autotrophic tissues the heteroglycans are essential for the nocturnal starch-sucrose conversion. In this review we summarize the current knowledge of these glycans, their interaction with glucosyl transferases and their possible cellular functions. We include data on the heteroglycans in heterotrophic plant tissues and discuss their role in intracellular carbon fluxes that originate from externally supplied carbohydrates.},
  language  = {en}
}
@article{BallLienardWattebledetal.2003,
  author    = {Ball, Steven G. and Li{\´e}nard, Luc and Wattebled, Fabrice and Steup, Martin and Hicks, Glenn and d'Hulst, Christophe},
  title     = {Defining the functions of maltodextrin active enzymes in starch metabolism in the unicellular alga Chlamydomonas reinhardtii},
  year      = {2003},
  language  = {en}
}
@article{SchmiederNitschkeSteupetal.2013,
  author    = {Schmieder, Peter and Nitschke, Felix and Steup, Martin and Mallow, Keven and Specker, Edgar},
  title     = {Determination of glucan phosphorylation using heteronuclear H-1,C-13 double and H-1,C-13,P-31 triple-resonance NMR spectra},
  series = {Magnetic resonance in chemistry},
  volume    = {51},
  journal   = {Magnetic resonance in chemistry},
  number    = {10},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0749-1581},
  doi       = {10.1002/mrc.3996},
  pages     = {655 -- 661},
  year      = {2013},
  abstract  = {Phosphorylation and dephosphorylation of starch and glycogen are important for their physicochemical properties and also their physiological functions. It is therefore desirable to reliably determine the phosphorylation sites. Heteronuclear multidimensional NMR-spectroscopy is in principle a straightforward analytical approach even for complex carbohydrate molecules. With heterogeneous samples from natural sources, however, the task becomes more difficult because a full assignment of the resonances of the carbohydrates is impossible to obtain. Here, we show that the combination of heteronuclear H-1,C-13 and H-1,C-13,P-31 techniques and information derived from spectra of a set of reference compounds can lead to an unambiguous determination of the phosphorylation sites even in heterogeneous samples.},
  language  = {en}
}
@article{RitteSteupKossmannetal.2003,
  author    = {Ritte, Gerhard and Steup, Martin and Kossmann, Jens and Lloyd, James R.},
  title     = {Determination of the starch phosphorylating enzyme activity in plant extracts},
  year      = {2003},
  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{MalinovaMahlowAlseekhetal.2014,
  author    = {Malinova, Irina and Mahlow, Sebastian and Alseekh, Saleh and Orawetz, Tom and Fernie, Alisdair R. and Baumann, Otto and Steup, Martin and Fettke, J{\"o}rg},
  title     = {Double knockout mutants of arabidopsis grown under normal conditions reveal that the plastidial phosphorylase isozyme participates in transitory starch metabolism},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {164},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {2},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.113.227843},
  pages     = {907 -- 921},
  year      = {2014},
  abstract  = {In leaves of two starch-related single-knockout lines lacking either the cytosolic transglucosidase (also designated as disproportionating enzyme 2, DPE2) or the maltose transporter (MEX1), the activity of the plastidial phosphorylase isozyme (PHS1) is increased. In both mutants, metabolism of starch-derived maltose is impaired but inhibition is effective at different subcellular sites. Two constitutive double knockout mutants were generated (designated as dpe2-1 x phs1a and mex1 x phs1b) both lacking functional PHS1. They reveal that in normally grown plants, the plastidial phosphorylase isozyme participates in transitory starch degradation and that the central carbon metabolism is closely integrated into the entire cell biology. All plants were grown either under continuous illumination or in a light-dark regime. Both double mutants were compromised in growth and, compared with the single knockout plants, possess less average leaf starch when grown in a light-dark regime. Starch and chlorophyll contents decline with leaf age. As revealed by transmission electron microscopy, mesophyll cells degrade chloroplasts, but degradation is not observed in plants grown under continuous illumination. The two double mutants possess similar but not identical phenotypes. When grown in a light-dark regime, mesophyll chloroplasts of dpe2-1 x phs1a contain a single starch granule but under continuous illumination more granules per chloroplast are formed. The other double mutant synthesizes more granules under either growth condition. In continuous light, growth of both double mutants is similar to that of the parental single knockout lines. Metabolite profiles and oligoglucan patterns differ largely in the two double mutants.},
  language  = {en}
}
@article{JueppnerMubeenLeisseetal.2017,
  author    = {J{\"u}ppner, Jessica and Mubeen, Umarah and Leisse, Andrea and Caldana, Camila and Brust, Henrike and Steup, Martin and Herrmann, Marion and Steinhauser, Dirk and Giavalisco, Patrick},
  title     = {Dynamics of lipids and metabolites during the cell cycle of Chlamydomonas reinhardtii},
  series = {The plant journal},
  volume    = {92},
  journal   = {The plant journal},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.13642},
  pages     = {331 -- 343},
  year      = {2017},
  abstract  = {Metabolites and lipids are the final products of enzymatic processes, distinguishing the different cellular functions and activities of single cells or whole tissues. Understanding these cellular functions within a well-established model system requires a systemic collection of molecular and physiological information. In the current report, the green alga Chlamydomonas reinhardtii was selected to establish a comprehensive workflow for the detailed multi-omics analysis of a synchronously growing cell culture system. After implementation and benchmarking of the synchronous cell culture, a two-phase extraction method was adopted for the analysis of proteins, lipids, metabolites and starch from a single sample aliquot of as little as 10-15million Chlamydomonas cells. In a proof of concept study, primary metabolites and lipids were sampled throughout the diurnal cell cycle. The results of these time-resolved measurements showed that single compounds were not only coordinated with each other in different pathways, but that these complex metabolic signatures have the potential to be used as biomarkers of various cellular processes. Taken together, the developed workflow, including the synchronized growth of the photoautotrophic cell culture, in combination with comprehensive extraction methods and detailed metabolic phenotyping has the potential for use in in-depth analysis of complex cellular processes, providing essential information for the understanding of complex biological systems.},
  language  = {en}
}
@article{HaebelAlbrechtSparbieretal.1998,
  author    = {Haebel, Sophie and Albrecht, Tanja and Sparbier, Katrin and Walden, Peter and K{\"o}rner, Roman and Steup, Martin},
  title     = {Electrophoresis-related protein modification: alkylation of carboxy residues revealed by mass spectrometry},
  year      = {1998},
  language  = {en}
}
@article{FettkeHejaziSmirnovaetal.2009,
  author    = {Fettke, J{\"o}rg and Hejazi, Mahdi and Smirnova, Julia and Hoechel, Erik and Stage, Marion and Steup, Martin},
  title     = {Eukaryotic starch degradation : integration of plastidial and cytosolic pathways},
  issn      = {0022-0957},
  doi       = {10.1093/Jxb/Erp054},
  year      = {2009},
  abstract  = {Starch is an important plant product widely used as a nutrient, as a source of renewable energy, and for many technological applications. In plants, starch is the almost ubiquitous storage carbohydrate whereas most heterotrophic prokaryotes and eukaryotes rely on glycogen. Despite close similarities in basic chemical features, starch and glycogen differ in both structural and physicochemical properties. Glycogen is a hydrosoluble macromolecule with evenly distributed branching points. Starch exists as a water-insoluble particle having a defined (and evolutionary conserved) internal structure. The biochemistry of starch requires the co-operation of up to 40 distinct (iso)enzymes whilst approximately 10 (iso)enzymes permit glycogen metabolism. The biosynthesis and degradation of native starch include the transition of carbohydrates from the soluble to the solid phase and vice versa. In this review, two novel aspects of the eukaryotic plastidial starch degradation are discussed: Firstly, biochemical reactions that take place at the surface of particulate glucans and mediate the phase transition of carbohydrates. Secondly, processes that occur downstream of the export of starch-derived sugars into the cytosol. Degradation of transitory starch mainly results in the formation of neutral sugars, such as glucose and maltose, that are transported into the cytosol via the respective translocators. The cytosolic metabolism of the neutral sugars includes the action of a hexokinase, a phosphoglucomutase, and a transglucosidase that utilizes high molecular weight glycans as a transient glucosyl acceptor or donor. Data are included on the transglucosidase (disproportionating isozyme 2) in Cyanophora paradoxa that accumulates storage carbohydrates in the cytosol rather than in the plastid.},
  language  = {en}
}
@article{MartinsHejaziFettkeetal.2013,
  author    = {Martins, Marina Camara Mattos and Hejazi, Mahdi and Fettke, J{\"o}rg and Steup, Martin and Feil, Regina and Krause, Ursula and Arrivault, Stephanie and Vosloh, Daniel and Figueroa, Carlos Maria and Ivakov, Alexander and Yadav, Umesh Prasad and Piques, Maria and Metzner, Daniela and Stitt, Mark and Lunn, John Edward},
  title     = {Feedback inhibition of starch degradation in arabidopsis leaves mediated by trehalose 6-phosphate},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {163},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.113.226787},
  pages     = {1142 -- 1163},
  year      = {2013},
  abstract  = {Many plants accumulate substantial starch reserves in their leaves during the day and remobilize them at night to provide carbon and energy for maintenance and growth. In this paper, we explore the role of a sugar-signaling metabolite, trehalose-6-phosphate (Tre6P), in regulating the accumulation and turnover of transitory starch in Arabidopsis (Arabidopsis thaliana) leaves. Ethanol-induced overexpression of trehalose-phosphate synthase during the day increased Tre6P levels up to 11-fold. There was a transient increase in the rate of starch accumulation in the middle of the day, but this was not linked to reductive activation of ADP-glucose pyrophosphorylase. A 2- to 3-fold increase in Tre6P during the night led to significant inhibition of starch degradation. Maltose and maltotriose did not accumulate, suggesting that Tre6P affects an early step in the pathway of starch degradation in the chloroplasts. Starch granules isolated from induced plants had a higher orthophosphate content than granules from noninduced control plants, consistent either with disruption of the phosphorylation-dephosphorylation cycle that is essential for efficient starch breakdown or with inhibition of starch hydrolysis by beta-amylase. Nonaqueous fractionation of leaves showed that Tre6P is predominantly located in the cytosol, with estimated in vivo Tre6P concentrations of 4 to 7 mu M in the cytosol, 0.2 to 0.5 mu M in the chloroplasts, and 0.05 mu M in the vacuole. It is proposed that Tre6P is a component in a signaling pathway that mediates the feedback regulation of starch breakdown by sucrose, potentially linking starch turnover to demand for sucrose by growing sink organs at night.},
  language  = {en}
}
@article{NakamuraOnoUtsumietal.2012,
  author    = {Nakamura, Yasunori and Ono, Masami and Utsumi, Chikako and Steup, Martin},
  title     = {Functional interaction between plastidial starch phosphorylase and starch branching enzymes from rice during the synthesis of branched maltodextrins},
  series = {Plant \& cell physiology},
  volume    = {53},
  journal   = {Plant \& cell physiology},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0032-0781},
  doi       = {10.1093/pcp/pcs030},
  pages     = {869 -- 878},
  year      = {2012},
  abstract  = {The present study established the way in which plastidial alpha-glucan phosphorylase (Pho1) synthesizes maltodextrin (MD) which can be the primer for starch biosynthesis in rice endosperm. The synthesis of MD by Pho1 was markedly accelerated by branching enzyme (BE) isozymes, although the greatest effect was exhibited by the presence of branching isozyme I (BEI) rather than by isozyme IIa (BEIIa) or isozyme IIb (BEIIb). The enhancement of the activity of Pho1 by BE was not merely due to the supply of a non-reducing ends. At the same time, Pho1 greatly enhanced the BE activity, possibly by generating a branched carbohydrate substrate which is used by BE with a higher affinity. The addition of isoamylase to the reaction mixture did not prevent the concerted action of Pho1 and BEI. Furthermore, in the product, the branched structure was, at least to some extent, maintained. Based on these results we propose that the interaction between Pho1 and BE is not merely due to chain-elongating and chain-branching reactions, but occurs in a physically and catalytically synergistic manner by each activating the mutual capacity of the other, presumably forming a physical association of Pho1, BEI and branched MDs. This close interaction might play a crucial role in the synthesis of branched MDs and the branched MDs can act as a primer for the biosynthesis of amylopectin molecules.},
  language  = {en}
}
@article{FettkeAlbrechtHejazietal.2010,
  author    = {Fettke, J{\"o}rg and Albrecht, Tanja and Hejazi, Mahdi and Mahlow, Sebastian and Nakamura, Yasunori and Steup, Martin},
  title     = {Glucose 1-phosphate is efficiently taken up by potato (Solanum tuberosum) tuber parenchyma cells and converted to reserve starch granules},
  issn      = {0028-646X},
  doi       = {10.1111/j.1469-8137.2009.03126.x},
  year      = {2010},
  abstract  = {Reserve starch is an important plant product but the actual biosynthetic process is not yet fully understood. Potato (Solanum tuberosum) tuber discs from various transgenic plants were used to analyse the conversion of external sugars or sugar derivatives to starch. By using in vitro assays, a direct glucosyl transfer from glucose 1-phosphate to native starch granules as mediated by recombinant plastidial phosphorylase was analysed. Compared with labelled glucose, glucose 6-phosphate or sucrose, tuber discs converted externally supplied [C-14] glucose 1-phosphate into starch at a much higher rate. Likewise, tuber discs from transgenic lines with a strongly reduced expression of cytosolic phosphoglucomutase, phosphorylase or transglucosidase converted glucose 1-phosphate to starch with the same or even an increased rate compared with the wild-type. Similar results were obtained with transgenic potato lines possessing a strongly reduced activity of both the cytosolic and the plastidial phosphoglucomutase. Starch labelling was, however, significantly diminished in transgenic lines, with a reduced concentration of the plastidial phosphorylase isozymes. Two distinct paths of reserve starch biosynthesis are proposed that explain, at a biochemical level, the phenotype of several transgenic plant lines.},
  language  = {en}
}
@article{FettkeMalinovaAlbrechtetal.2011,
  author    = {Fettke, J{\"o}rg and Malinova, Irina and Albrecht, Tanja and Hejazi, Mahdi and Steup, Martin},
  title     = {Glucose-1-Phosphate transport into protoplasts and chloroplasts from leaves of arabidopsis},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {155},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {4},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.110.168716},
  pages     = {1723 -- 1734},
  year      = {2011},
  abstract  = {Almost all glucosyl transfer reactions rely on glucose-1-phosphate (Glc-1-P) that either immediately acts as glucosyl donor or as substrate for the synthesis of the more widely used Glc dinucleotides, ADPglucose or UDPglucose. In this communication, we have analyzed two Glc-1-P-related processes: the carbon flux from externally supplied Glc-1-P to starch by either mesophyll protoplasts or intact chloroplasts from Arabidopsis (Arabidopsis thaliana). When intact protoplasts or chloroplasts are incubated with [U-C-14]Glc-1-P, starch is rapidly labeled. Incorporation into starch is unaffected by the addition of unlabeled Glc-6-P or Glc, indicating a selective flux from Glc-1-P to starch. However, illuminated protoplasts incorporate less C-14 into starch when unlabeled bicarbonate is supplied in addition to the C-14-labeled Glc-1-P. Mesophyll protoplasts incubated with [U-C-14] Glc-1-P incorporate C-14 into the plastidial pool of adenosine diphosphoglucose. Protoplasts prepared from leaves of mutants of Arabidopsis that lack either the plastidial phosphorylase or the phosphoglucomutase isozyme incorporate C-14 derived from external Glc-1-P into starch, but incorporation into starch is insignificant when protoplasts from a mutant possessing a highly reduced ADPglucose pyrophosphorylase activity are studied. Thus, the path of assimilatory starch biosynthesis initiated by extraplastidial Glc-1-P leads to the plastidial pool of adenosine diphosphoglucose, and at this intermediate it is fused with the Calvin cycle-driven route. Mutants lacking the plastidial phosphoglucomutase contain a small yet significant amount of transitory starch.},
  language  = {en}
}
@article{AlbrechtGrevePuschetal.1998,
  author    = {Albrecht, Tanja and Greve, Burkhard and Pusch, Kerstin and Koßmann, Jens and Buchner, Peter and Wobus, Ulrich and Steup, Martin},
  title     = {Homo- and Heterodimers of Pho1-Type Phosphorylase Isoforms in Solanum tuberosum L. as Revealed by Sequence- Specific Antibodies},
  year      = {1998},
  language  = {en}
}
@article{NitschkeWangSchmiederetal.2013,
  author    = {Nitschke, Felix and Wang, Peixiang and Schmieder, Peter and Girard, Jean-Marie and Awrey, Donald E. and Wang, Tony and Israelian, Johan and Zhao, XiaoChu and Turnbull, Julie and Heydenreich, Matthias and Kleinpeter, Erich and Steup, Martin and Minassian, Berge A.},
  title     = {Hyperphosphorylation of glucosyl C6 carbons and altered structure of glycogen in the neurodegenerative epilepsy lafora disease},
  series = {Cell metabolism},
  volume    = {17},
  journal   = {Cell metabolism},
  number    = {5},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {1550-4131},
  doi       = {10.1016/j.cmet.2013.04.006},
  pages     = {756 -- 767},
  year      = {2013},
  abstract  = {Laforin or malin deficiency causes Lafora disease, characterized by altered glycogen metabolism and teenage-onset neurodegeneration with intractable and invariably fatal epilepsy. Plant starches possess small amounts of metabolically essential monophosphate esters. Glycogen contains similar phosphate amounts, which are thought to originate from a glycogen synthase error side reaction and therefore lack any specific function. Glycogen is also believed to lack monophosphates at glucosyl carbon C6, an essential phosphorylation site in plant starch metabolism. We now show that glycogen phosphorylation is not due to a glycogen synthase side reaction, that C6 is a major glycogen phosphorylation site, and that C6 monophosphates predominate near centers of glycogen molecules and positively correlate with glycogen chain lengths. Laforin or malin deficiency causes C6 hyperphosphorylation, which results in malformed long-chained glycogen that accumulates in many tissues, causing neurodegeneration in brain. Our work advances the understanding of Lafora disease pathogenesis and suggests that glycogen phosphorylation has important metabolic function.},
  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{FettkeNunesNesiFernieetal.2011,
  author    = {Fettke, J{\"o}rg and Nunes-Nesi, Adriano and Fernie, Alisdair R. and Steup, Martin},
  title     = {Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana},
  series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants},
  volume    = {168},
  journal   = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants},
  number    = {12},
  publisher = {Elsevier},
  address   = {Jena},
  issn      = {0176-1617},
  doi       = {10.1016/j.jplph.2010.09.008},
  pages     = {1415 -- 1425},
  year      = {2011},
  abstract  = {Plastidial degradation of transitory starch yields mainly maltose and glucose. Following the export into the cytosol, maltose acts as donor for a glucosyl transfer to cytosolic heteroglycans as mediated by a cytosolic transglucosidase (DPE2; EC 2.4.1.25) and the second glucosyl residue is liberated as glucose. The cytosolic phosphorylase (Pho2/PHS2; EC 2.4.1.1) also interacts with heteroglycans using the same intramolecular sites as DPE2. Thus, the two glucosyl transferases interconnect the cytosolic pools of glucose and glucose 1-phosphate. Due to the complex monosaccharide pattern, other heteroglycan-interacting proteins (Hips) are expected to exist. Identification of those proteins was approached by using two types of affinity chromatography. Heteroglycans from leaves of Arabidopsis thaliana (Col-0) covalently bound to Sepharose served as ligands that were reacted with a complex mixture of buffer-soluble proteins from Arabidopsis leaves. Binding proteins were eluted by sodium chloride. For identification, SDS-PAGE, tryptic digestion and MALDI-TOF analyses were applied. A strongly interacting polypeptide (approximately 40 kDa; designated as HIP1.3) was observed as product of locus At1g09340. Arabidopsis mutants deficient in HIP1.3 were reduced in growth and contained heteroglycans displaying an altered monosaccharide pattern. Wild type plants express HIP1.3 most strongly in leaves. As revealed by immuno fluorescence, HIP1.3 is located in the cytosol of mesophyll cells but mostly associated with the cytosolic surface of the chloroplast envelope membranes. In an HIP1.3-deficient mutant the immunosignal was undetectable. Metabolic profiles from leaves of this mutant and wild type plants as well were determined by GC-MS. As compared to the wild type control, more than ten metabolites, such as ascorbic acid, fructose, fructose bisphosphate, glucose, glycine, were elevated in darkness but decreased in the light. Although the biochemical function of HIP1.3 has not yet been elucidated, it is likely to possess an important function in the central carbon metabolism of higher plants.},
  language  = {en}
}
@article{EckermannFettkeSteup2002,
  author    = {Eckermann, Nora and Fettke, J{\"o}rg and Steup, Martin},
  title     = {Identification of polysaccharide binding proteins by affinity electrophoresis in inhomogeneous polyacrylamide gels and subsequent SDS-PAGE/MALDI-TOF analysis},
  year      = {2002},
  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{DuwenigSteupKossmann1997,
  author    = {Duwenig, Elke and Steup, Martin and Kossmann, Jens},
  title     = {Induction of genes encoding plastidic phosphorylase from spinach (Spinacia oleracea L.) and potato (Solanum tuberosum L.) by exogenously supplied carbohydrates in excised leaf discs},
  year      = {1997},
  language  = {en}
}
@article{SchwarteBrustSteupetal.2013,
  author    = {Schwarte, Sandra and Brust, Henrike and Steup, Martin and Tiedemann, Ralph},
  title     = {Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana},
  doi       = {10.1186/1756-0500-6-84},
  year      = {2013},
  language  = {en}
}
@misc{SchwarteBrustSteupetal.2013,
  author    = {Schwarte, Sandra and Brust, Henrike and Steup, Martin and Tiedemann, Ralph},
  title     = {Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana},
  series = {BMC Research Notes},
  journal   = {BMC Research Notes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401128},
  pages     = {14},
  year      = {2013},
  abstract  = {Background Natural accessions of Arabidopsis thaliana are a well-known system to measure levels of intraspecific genetic variation. Leaf starch content correlates negatively with biomass. Starch is synthesized by the coordinated action of many (iso)enzymes. Quantitatively dominant is the repetitive transfer of glucosyl residues to the non-reducing ends of α-glucans as mediated by starch synthases. In the genome of A. thaliana, there are five classes of starch synthases, designated as soluble starch synthases (SSI, SSII, SSIII, and SSIV) and granule-bound synthase (GBSS). Each class is represented by a single gene. The five genes are homologous in functional domains due to their common origin, but have evolved individual features as well. Here, we analyze the extent of genetic variation in these fundamental protein classes as well as possible functional implications on transcript and protein levels. Findings Intraspecific sequence variation of the five starch synthases was determined by sequencing the entire loci including promoter regions from 30 worldwide distributed accessions of A. thaliana. In all genes, a considerable number of nucleotide polymorphisms was observed, both in non-coding and coding regions, and several amino acid substitutions were identified in functional domains. Furthermore, promoters possess numerous polymorphisms in potentially regulatory cis-acting regions. By realtime experiments performed with selected accessions, we demonstrate that DNA sequence divergence correlates with significant differences in transcript levels. Conclusions Except for AtSSII, all starch synthase classes clustered into two or three groups of haplotypes, respectively. Significant difference in transcript levels among haplotype clusters in AtSSIV provides evidence for cis-regulation. By contrast, no such correlation was found for AtSSI, AtSSII, AtSSIII, and AtGBSS, suggesting trans-regulation. The expression data presented here point to a regulation by common trans-regulatory transcription factors which ensures a coordinated action of the products of these four genes during starch granule biosynthesis. The apparent cis-regulation of AtSSIV might be related to its role in the initiation of de novo biosynthesis of granules.},
  language  = {en}
}
@article{PaparelliGonzaliParlantietal.2012,
  author    = {Paparelli, Eleonora and Gonzali, Silvia and Parlanti, Sandro and Novi, Giacomo and Giorgi, Federico M. and Licausi, Francesco and Kosmacz, Monika and Feil, Regina and Lunn, John Edward and Brust, Henrike and van Dongen, Joost T. and Steup, Martin and Perata, Pierdomenico},
  title     = {Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in arabidopsis},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {160},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.112.204016},
  pages     = {1237 -- 1250},
  year      = {2012},
  abstract  = {The crucial role of carbohydrate in plant growth and morphogenesis is widely recognized. In this study, we describe the characterization of nana, a dwarf Arabidopsis (Arabidopsis thaliana) mutant impaired in carbohydrate metabolism. We show that the nana dwarf phenotype was accompanied by altered leaf morphology and a delayed flowering time. Our genetic and molecular data indicate that the mutation in nana is due to a transfer DNA insertion in the promoter region of a gene encoding a chloroplast-located aspartyl protease that alters its pattern of expression. Overexpression of the gene (oxNANA) phenocopies the mutation. Both nana and oxNANA display alterations in carbohydrate content, and the extent of these changes varies depending on growth light intensity. In particular, in low light, soluble sugar levels are lower and do not show the daily fluctuations observed in wild-type plants. Moreover, nana and oxNANA are defective in the expression of some genes implicated in sugar metabolism and photosynthetic light harvesting. Interestingly, some chloroplast-encoded genes as well as genes whose products seem to be involved in retrograde signaling appear to be down-regulated. These findings suggest that the NANA aspartic protease has an important regulatory function in chloroplasts that not only influences photosynthetic carbon metabolism but also plastid and nuclear gene expression.},
  language  = {en}
}
@article{NakamuraSteupColleonietal.2022,
  author    = {Nakamura, Yasunori and Steup, Martin and Colleoni, Christophe and Iglesias, Alberto A. and Bao, Jinsong and Fujita, Naoko and Tetlow, Ian},
  title     = {Molecular regulation of starch metabolism},
  series = {Plant molecular biology : an international journal of fundamental research and genetic engineering},
  volume    = {108},
  journal   = {Plant molecular biology : an international journal of fundamental research and genetic engineering},
  number    = {4-5},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0167-4412},
  doi       = {10.1007/s11103-022-01253-0},
  pages     = {289 -- 290},
  year      = {2022},
  language  = {en}
}
@article{WernerBehrsingScharteetal.2002,
  author    = {Werner, Deljana and Behrsing, Olaf and Scharte, Gudrun and Woller, Jochen and Steup, Martin and Micheel, Burkhard},
  title     = {Monoclonal anti-diuron antibodies prevent inhibition of photosynthesis by diuron},
  year      = {2002},
  language  = {en}
}
@article{GrunwaldtHaebelSpitzetal.2002,
  author    = {Grunwaldt, Gisela and Haebel, Sophie and Spitz, Christian and Steup, Martin and Menzel, Ralf},
  title     = {Multiple binding sites of fluorescein isothiocyanate moieties on myoglobin : photophysical heterogeneity as revealed by ground- and excited-state spectroscopy},
  issn      = {1011-1344},
  year      = {2002},
  language  = {en}
}
@article{DeschampsHaferkampDauvilleeetal.2006,
  author    = {Deschamps, Philippe and Haferkamp, Ilka and Dauvillee, David and Haebel, Sophie and Steup, Martin and Buleon, Alain and Putaux, Jean-Luc and Colleoni, Christophe and d'Hulst, Christophe and Plancke, Charlotte and Gould, Sven and Maier, Uwe and Neuhaus, Heinz Eckhard and Ball, Steven G.},
  title     = {Nature of the periplastidial pathway of starch synthesis in the cryptophyte Guillardia theta},
  issn      = {1535-9778},
  doi       = {10.1128/Ec.00380-05},
  year      = {2006},
  abstract  = {The nature of the periplastidial pathway of starch biosynthesis was investigated with the model cryptophyte Guillardia theta. The storage polysaccharide granules were shown to be composed of both amylose and amylopectin fractions with a chain length distribution and crystalline organization very similar to those of starch from green algae and land plants. Most starch granules displayed a shape consistent with biosynthesis occurring around the pyrenoid through the rhodoplast membranes. A protein with significant similarity to the amylose-synthesizing granule-bound starch syntbase 1 from green plants was found as the major polypeptide bound to the polysaccharide matrix. N-terminal sequencing of the mature protein proved that the precursor protein carries a nonfunctional transit peptide in its bipartite topogenic signal sequence which is cleaved without yielding transport of the enzyme across the two inner plastid membranes. The enzyme was shown to display similar affinities for ADP and UDP-glucose, while the V-max measured with UDP-glucose was twofold higher. The granule-bound starch synthase from Guillardia theta was demonstrated to be responsible for the synthesis of long glucan chains and therefore to be the functional equivalent of the amylose- synthesizing enzyme of green plants. Preliminary characterization of the starch pathway suggests that Guillardia theta utilizes a UDP-glucose-based pathway to synthesize starch},
  language  = {en}
}
@article{StahlThurlZengetal.1994,
  author    = {Stahl, Bernd and Thurl, Stephan and Zeng, Jianru and Karas, Michael and Hillenkamp, Franz and Steup, Martin and Sawatzki, G{\"u}nther},
  title     = {Oligosaccharides from human milk as revealed by matrix-assisted laser desorption : ionization mass spectrometry},
  year      = {1994},
  language  = {en}
}
@misc{SullivanNitschkeSteupetal.2017,
  author    = {Sullivan, Mitchell A. and Nitschke, Silvia and Steup, Martin and Minassian, Berge A. and Nitschke, Felix},
  title     = {Pathogenesis of Lafora disease},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1080},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47462},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-474622},
  pages     = {18},
  year      = {2017},
  abstract  = {Lafora disease (LD, OMIM \#254780) is a rare, recessively inherited neurodegenerative disease with adolescent onset, resulting in progressive myoclonus epilepsy which is fatal usually within ten years of symptom onset. The disease is caused by loss-of-function mutations in either of the two genes EPM2A (laforin) or EPM2B (malin). It characteristically involves the accumulation of insoluble glycogen-derived particles, named Lafora bodies (LBs), which are considered neurotoxic and causative of the disease. The pathogenesis of LD is therefore centred on the question of how insoluble LBs emerge from soluble glycogen. Recent data clearly show that an abnormal glycogen chain length distribution, but neither hyperphosphorylation nor impairment of general autophagy, strictly correlates with glycogen accumulation and the presence of LBs. This review summarizes results obtained with patients, mouse models, and cell lines and consolidates apparent paradoxes in the LD literature. Based on the growing body of evidence, it proposes that LD is predominantly caused by an impairment in chain-length regulation affecting only a small proportion of the cellular glycogen. A better grasp of LD pathogenesis will further develop our understanding of glycogen metabolism and structure. It will also facilitate the development of clinical interventions that appropriately target the underlying cause of LD.},
  language  = {en}
}
@article{RitteHeydenreichMahlowetal.2006,
  author    = {Ritte, Gerhard and Heydenreich, Matthias and Mahlow, Sebastian and Haebel, Sophie and Koetting, Oliver and Steup, Martin},
  title     = {Phosphorylation of C6- and C3-positions of glucosyl residues in starch is catalysed by distinct dikinases},
  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    = {20},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0014-5793},
  doi       = {10.1016/j.febslet.2006.07.085},
  pages     = {4872 -- 4876},
  year      = {2006},
  abstract  = {Glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD) are required for normal starch metabolism. We analysed starch phosphorylation in Arabidopsis wildtype plants and mutants lacking either GWD or PWD using P-31 NMR. Phosphorylation at both C6- and C3-positions of glucose moieties in starch was drastically decreased in GWD-deficient mutants. In starch from PWD-deficient plants C3-bound phosphate was reduced to levels close to the detection limit. The latter result contrasts with previous reports according to which GWD phosphorylates both C6- and C3-positions. In these studies, phosphorylation had been analysed by HPLC of acid-hydrolysed glucans. We now show that maltose-6-phosphate, a product of incomplete starch hydrolysis, co-eluted with glucose-3-phosphate under the chromatographic conditions applied. Re-examination of the specificity of the dikinases using an improved method demonstrates that C6- and C3-phosphorylation is selectively catalysed by GWD and PWD, respectively.},
  language  = {en}
}
@article{RitteScharfEckermannetal.2004,
  author    = {Ritte, Gerhard and Scharf, Anke and Eckermann, Nora and Haebel, Sophie and Steup, Martin},
  title     = {Phosphorylation of transitory starch is increased during degradation},
  year      = {2004},
  abstract  = {The starch excess phenotype of Arabidopsis mutants defective in the starch phosphorylating enzyme glucan, water dikinase (EC 2.7.9.4) indicates that phosphorylation of starch is required for its degradation. However, the underlying mechanism has not yet been elucidated. In this study, two in vivo systems have been established that allow the analysis of phosphorylation of transitory starch during both biosynthesis in the light and degradation in darkness. First, a photoautotrophic culture of the unicellular green alga Chlamydomonas reinhardtii was used to monitor the incorporation of exogenously supplied P-32 orthophosphate into starch. Illuminated cells incorporated P-32 into starch with a constant rate during 2 h. By contrast, starch phosphorylation in darkened cells exceeded that in illuminated cells within the first 30 min, but subsequently phosphate incorporation declined. Pulse-chase experiments performed with P-32/P-31 orthophosphate revealed a high turnover of the starch-bound phosphate esters in darkened cells but no detectable turnover in illuminated cells. Secondly, leaf starch granules were isolated from potato (Solanum tuberosum) plants grown under controlled conditions and glucan chains from the outer granule layer were released by isoamylase. Phosphorylated chains were purified and analyzed using high performance anion-exchange chromatography and matrix-assisted laser desorption/ionization mass spectrometry. Glucans released from the surface of starch granules that had been isolated from darkened leaves possessed a considerably higher degree of phosphorylation than those prepared from leaves harvested during the light period. Thus, in the unicellular alga as well as in potato leaves, net starch degradation is accompanied with an increased phosphorylation of starch},
  language  = {en}
}
@article{SmirnovaFernieSpahnetal.2017,
  author    = {Smirnova, Julia and Fernie, Alisdair R. and Spahn, Christian M. T. and Steup, Martin},
  title     = {Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants},
  series = {Analytical biochemistry : methods in the biological sciences},
  volume    = {532},
  journal   = {Analytical biochemistry : methods in the biological sciences},
  publisher = {Elsevier},
  address   = {San Diego},
  issn      = {0003-2697},
  doi       = {10.1016/j.ab.2017.05.026},
  pages     = {72 -- 82},
  year      = {2017},
  abstract  = {Maltose frequently occurs as intermediate of the central carbon metabolism of prokaryotic and eukaryotic cells. Various mutants possess elevated maltose levels. Maltose exists as two anomers, (alpha- and beta-form) which are rapidly interconverted without requiring enzyme-mediated catalysis. As maltose is often abundant together with other oligoglucans, selective quantification is essential. In this communication, we present a photometric maltose assay using 4-alpha-glucanotransferase (AtDPE2) from Arabidopsis thaliana. Under in vitro conditions, AtDPE2 utilizes maltose as glucosyl donor and glycogen as acceptor releasing the other hexosyl unit as free glucose which is photometrically quantified following enzymatic phosphorylation and oxidation. Under the conditions used, DPE2 does not noticeably react with other di- or oligosaccharides. Selectivity compares favorably with that of maltase frequently used in maltose assays. Reducing end interconversion of the two maltose anomers is in rapid equilibrium and, therefore, the novel assay measures total maltose contents. Furthermore, an AtDPE2-based continuous photometric assay is presented which allows to quantify beta-amylase activity and was found to be superior to a conventional test. Finally, the AtDPE2-based maltose assay was used to quantify leaf maltose contents of both Arabidopsis wild type and AtDPE2-deficient plants throughout the light-dark cycle. These data are presented together with assimilatory starch levels. (C) 2017 Published by Elsevier Inc.},
  language  = {en}
}
@article{DauvilleeChochoisSteupetal.2006,
  author    = {Dauvillee, David and Chochois, Vincent and Steup, Martin and Haebel, Sophie and Eckermann, Nora and Ritte, Gerhard and Ral, Jean-Philippe and Colleoni, Christophe and Hicks, Glenn and Wattebled, Fabrice and Deschamps, Philippe and Lienard, Luc and Cournac, Laurent and Putaux, Jean-Luc and Dupeyre, Danielle and Ball, Steven G.},
  title     = {Plastidial phosphorylase is required for normal starch synthesis in Chlamydomonas reinhardtii},
  series = {The plant journal},
  volume    = {48},
  journal   = {The plant journal},
  number    = {2},
  publisher = {Blackwell},
  address   = {Oxford},
  issn      = {0960-7412},
  doi       = {10.1111/j.1365-313X.2006.02870.x},
  pages     = {274 -- 285},
  year      = {2006},
  abstract  = {Among the three distinct starch phosphorylase activities detected in Chlamydomonas reinhardtii, two distinct plastidial enzymes (PhoA and PhoB) are documented while a single extraplastidial form (PhoC) displays a higher affinity for glycogen as in vascular plants. The two plastidial phosphorylases are shown to function as homodimers containing two 91-kDa (PhoA) subunits and two 110-kDa (PhoB) subunits. Both lack the typical 80-amino-acid insertion found in the higher plant plastidial forms. PhoB is exquisitely sensitive to inhibition by ADP-glucose and has a low affinity for malto-oligosaccharides. PhoA is more similar to the higher plant plastidial phosphorylases: it is moderately sensitive to ADP-glucose inhibition and has a high affinity for unbranched malto-oligosaccharides. Molecular analysis establishes that STA4 encodes PhoB. Chlamydomonas reinhardtii strains carrying mutations at the STA4 locus display a significant decrease in amounts of starch during storage that correlates with the accumulation of abnormally shaped granules containing a modified amylopectin structure and a high amylose content. The wild-type phenotype could be rescued by reintroduction of the cloned wild-type genomic DNA, thereby demonstrating the involvement of phosphorylase in storage starch synthesis.},
  language  = {en}
}