@misc{ApriyantoCompartFettke2022,
  author    = {Apriyanto, Ardha and Compart, Julia and Fettke, J{\"o}rg},
  title     = {A review of starch, a unique biopolymer - structure, metabolism and in planta modifications},
  series = {Plant science : an international journal of experimental plant biology},
  volume    = {318},
  journal   = {Plant science : an international journal of experimental plant biology},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0168-9452},
  doi       = {10.1016/j.plantsci.2022.111223},
  pages     = {8},
  year      = {2022},
  abstract  = {Starch is a complex carbohydrate polymer produced by plants and especially by crops in huge amounts. It consists of amylose and amylopectin, which have alpha-1,4-and alpha-1,6-linked glucose units. Despite this simple chemistry, the entire starch metabolism is complex, containing various (iso)enzymes/proteins. However, whose interplay is still not yet fully understood. Starch is essential for humans and animals as a source of nutrition and energy. Nowadays, starch is also commonly used in non-food industrial sectors for a variety of purposes. However, native starches do not always satisfy the needs of a wide range of (industrial) applications. This review summarizes the structural properties of starch, analytical methods for starch characterization, and in planta starch modifications.},
  language  = {en}
}
@article{ApriyantoCompartZimmermannetal.2022,
  author    = {Apriyanto, Ardha and Compart, Julia and Zimmermann, Vincent and Alseekh, Saleh and Fernie, Alisdair and Fettke, J{\"o}rg},
  title     = {Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.)},
  series = {Food chemistry},
  volume    = {393},
  journal   = {Food chemistry},
  publisher = {Elsevier},
  address   = {New York, NY [u.a.]},
  issn      = {0308-8146},
  doi       = {10.1016/j.foodchem.2022.133361},
  pages     = {11},
  year      = {2022},
  abstract  = {Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield.},
  language  = {en}
}
@phdthesis{FloresCastellanos2023,
  author    = {Flores Castellanos, Junio},
  title     = {Potato tuber (Solanum tuberosum L. cv Desiree) — characterization of starch interacting proteins and maltodextrin metabolism},
  doi       = {10.25932/publishup-61505},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-615055},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XV, 69},
  year      = {2023},
  abstract  = {Starch is a biopolymer for which, despite its simple composition, understanding the precise mechanism behind its formation and regulation has been challenging. Several approaches and bioanalytical tools can be used to expand the knowledge on the different parts involved in the starch metabolism. In this sense, a comprehensive analysis targeting two of the main groups of molecules involved in this process: proteins, as effectors/regulators of the starch metabolism, and maltodextrins as starch components and degradation products, was conducted in this research work using potato plants (Solanum tuberosum L. cv. Desiree) as model of study. On one side, proteins physically interacting to potato starch were isolated and analyzed through mass spectrometry and western blot for their identification. Alternatively, starch interacting proteins were explored in potato tubers from transgenic plants having antisense inhibition of starch-related enzymes and on tubers stored under variable environmental conditions. Most of the proteins recovered from the starch granules corresponded to previously described proteins having a specific role in the starch metabolic pathway. Another set of proteins could be grouped as protease inhibitors, which were found weakly interacting to starch. Variations in the protein profile obtained after electrophoresis separation became clear when tubers were stored under different temperatures, indicating a differential expression of proteins in response to changing environmental conditions. On the other side, since maltodextrin metabolism is thought to be involved in both starch initiation and degradation, soluble maltooligosaccharide content in potato tubers was analyzed in this work under diverse experimental variables. For this, tuber disc samples from wild type and transgenic lines strongly repressing either the plastidial or cytosolic form of the -glucan phosphorylase and phosphoglucomutase were incubated with glucose, glucose-6-phosphate, and glucose-1-phosphate solutions to evaluate the influence of such enzymes on the conversion of the carbon sources into soluble maltodextrins, in comparison to wild-type samples. Relative maltodextrin amounts analyzed through capillary electrophoresis equipped with laser-induced fluorescence (CE-LIF) revealed that tuber discs could immediately uptake glucose-1-phosphate and use it to produce maltooligosaccharides with a degree of polymerization of up to 30 (DP30), in contrast to transgenic tubers with strong repression of the plastidial glucan phosphorylase. The results obtained from the maltodextrin analysis support previous indications that a specific transporter for glucose-1-phosphate may exist in both the plant cells and the plastidial membranes, thereby allowing a glucose-6-phosphate independent transport. Furthermore, it confirms that the plastidial glucan phosphorylase is responsible for producing longer maltooligosaccharides in the plastids by catalyzing a glucan polymerization reaction when glucose-1-phosphate is available. All these findings contribute to a better understanding of the role of the plastidial glucan phosphorylase as a key enzyme directly involved in the synthesis and degradation of glucans and their implication on starch metabolism.},
  language  = {en}
}
@article{MeridaFettke2021,
  author    = {Merida, Angel and Fettke, J{\"o}rg},
  title     = {Starch granule initiation in Arabidopsis thaliana chloroplasts},
  series = {The plant journal},
  volume    = {107},
  journal   = {The plant journal},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.15359},
  pages     = {688 -- 697},
  year      = {2021},
  abstract  = {The initiation of starch granule formation and the mechanism controlling the number of granules per plastid have been some of the most elusive aspects of starch metabolism. This review covers the advances made in the study of these processes. The analyses presented herein depict a scenario in which starch synthase isoform 4 (SS4) provides the elongating activity necessary for the initiation of starch granule formation. However, this protein does not act alone; other polypeptides are required for the initiation of an appropriate number of starch granules per chloroplast. The functions of this group of polypeptides include providing suitable substrates (maltooligosaccharides) to SS4, the localization of the starch initiation machinery to the thylakoid membranes, and facilitating the correct folding of SS4. The number of starch granules per chloroplast is tightly regulated and depends on the developmental stage of the leaves and their metabolic status. Plastidial phosphorylase (PHS1) and other enzymes play an essential role in this process since they are necessary for the synthesis of the substrates used by the initiation machinery. The mechanism of starch granule formation initiation in Arabidopsis seems to be generalizable to other plants and also to the synthesis of long-term storage starch. The latter, however, shows specific features due to the presence of more isoforms, the absence of constantly recurring starch synthesis and degradation, and the metabolic characteristics of the storage sink organs.},
  language  = {en}
}
@phdthesis{Apriyanto2023,
  author    = {Apriyanto, Ardha},
  title     = {Analysis of starch metabolism in source and sink tissue of plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {166},
  year      = {2023},
  abstract  = {Starch is an essential biopolymer produced by plants. Starch can be made inside source tissue (such as leaves) and sink tissue (such as fruits and tubers). Nevertheless, understanding how starch metabolism is regulated in source and sink tissues is fundamental for improving crop production. Despite recent advances in the understanding of starch and its metabolism, there is still a knowledge gap in the source and sink metabolism. Therefore, this study aimed to summarize the state of the art regarding starch structure and metabolism inside plants. In addition, this study aimed to elucidate the regulation of starch metabolism in the source tissue using the leaves of a model organism, Arabidopsis thaliana, and the sink tissue of oil palm (Elaeis guineensis) fruit as a commercial crop. The research regarding the source tissue will focus on the effect of the blockage of starch degradation on the starch parameter in leaves, especially in those of A. thaliana, which lack both disproportionating enzyme 2 (DPE2) and plastidial glucan phosphorylase 1 (PHS1) (dpe2/phs1). The additional elimination of phosphoglucan water dikinase (PWD), starch excess 4 (SEX4), isoamylase 3 (ISA3), and disproportionating enzyme 1 (DPE1) in the dpe2/phs1 mutant background demonstrates the alteration of starch granule number per chloroplast. This study provides insights into the control mechanism of granule number regulation in the chloroplast. The research regarding the sink tissue will emphasize the relationship between starch metabolism and the lipid metabolism pathway in oil palm fruits. This study was conducted to observe the alteration of starch parameters, metabolite abundance, and gene expression during oil palm fruit development with different oil yields. This study shows that starch and sucrose can be used as biomarkers for oil yield in oil palms. In addition, it is revealed that the enzyme isoforms related to starch metabolism influence the oil production in oil palm fruit. Overall, this thesis presents novel information regarding starch metabolism in the source tissue of A.thaliana and the sink tissue of E.guineensis. The results shown in this thesis can be applied to many applications, such as modifying the starch parameter in other plants for specific needs.},
  language  = {en}
}
@article{SinghCompartALRawietal.2022,
  author    = {Singh, Aakanksha and Compart, Julia and AL-Rawi, Shadha Abduljaleel and Mahto, Harendra and Ahmad, Abubakar Musa and Fettke, J{\"o}rg},
  title     = {LIKE EARLY STARVATION 1 alters the glucan structures at the starch granule surface and thereby influences the action of both starch-synthesizing and starch-degrading enzymes},
  series = {The plant journal},
  volume    = {111},
  journal   = {The plant journal},
  number    = {3},
  publisher = {Wiley-Blackwell},
  address   = {Oxford},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.15855},
  pages     = {819 -- 835},
  year      = {2022},
  abstract  = {For starch metabolism to take place correctly, various enzymes and proteins acting on the starch granule surface are crucial. Recently, two non-catalytic starch-binding proteins, pivotal for normal starch turnover in Arabidopsis leaves, namely, EARLY STARVATION 1 (ESV1) and its homolog LIKE EARLY STARVATION 1 (LESV), have been identified. Both share nearly 38\% sequence homology. As ESV1 has been found to influence glucan phosphorylation via two starch-related dikinases, alpha-glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD), through modulating the surface glucan structures of the starch granules and thus affecting starch degradation, we assess the impact of its homolog LESV on starch metabolism. Thus, the 65-kDa recombinant protein LESV and the 50-kDa ESV1 were analyzed regarding their influence on the action of GWD and PWD on the surface of the starch granules. We included starches from various sources and additionally assessed the effect of these non-enzymatic proteins on other starch-related enzymes, such as starch synthases (SSI and SSIII), starch phosphorylases (PHS1), isoamylase and beta-amylase. The data obtained indicate that starch phosphorylation, hydrolyses and synthesis were affected by LESV and ESV1. Furthermore, incubation with LESV and ESV1 together exerted an additive effect on starch phosphorylation. In addition, a stable alteration of the glucan structures at the starch granule surface following treatment with LESV and ESV1 was observed. Here, we discuss all the observed changes that point to modifications in the glucan structures at the surface of the native starch granules and present a model to explain the existing processes.},
  language  = {en}
}
@article{BrustOrzechowskiFettke2020,
  author    = {Brust, Henrike and Orzechowski, Slawomir and Fettke, J{\"o}rg},
  title     = {Starch and Glycogen Analyses},
  series = {Biomolecules},
  volume    = {10},
  journal   = {Biomolecules},
  number    = {7},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2218-273X},
  doi       = {10.3390/biom10071020},
  pages     = {24},
  year      = {2020},
  abstract  = {For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included},
  language  = {en}
}
@misc{BrustOrzechowskiFettke2020,
  author    = {Brust, Henrike and Orzechowski, Slawomir and Fettke, J{\"o}rg},
  title     = {Starch and Glycogen Analyses},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1004},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47805},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-478054},
  pages     = {26},
  year      = {2020},
  abstract  = {For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included},
  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}
}
@article{AnnunziataApeltCarilloetal.2017,
  author    = {Annunziata, Maria Grazia and Apelt, Federico and Carillo, Petronia and Krause, Ursula and Feil, Regina and Mengin, Virginie and Lauxmann, Martin A. and Koehl, Karin and Nikoloski, Zoran and Stitt, Mark and Lunn, John Edward},
  title     = {Getting back to nature: a reality check for experiments in controlled environments},
  series = {Journal of experimental botany},
  volume    = {68},
  journal   = {Journal of experimental botany},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0022-0957},
  doi       = {10.1093/jxb/erx220},
  pages     = {4463 -- 4477},
  year      = {2017},
  abstract  = {Irradiance from sunlight changes in a sinusoidal manner during the day, with irregular fluctuations due to clouds, and light-dark shifts at dawn and dusk are gradual. Experiments in controlled environments typically expose plants to constant irradiance during the day and abrupt light-dark transitions. To compare the effects on metabolism of sunlight versus artificial light regimes, Arabidopsis thaliana plants were grown in a naturally illuminated greenhouse around the vernal equinox, and in controlled environment chambers with a 12-h photoperiod and either constant or sinusoidal light profiles, using either white fluorescent tubes or light-emitting diodes (LEDs) tuned to a sunlight-like spectrum as the light source. Rosettes were sampled throughout a 24-h diurnal cycle for metabolite analysis. The diurnal metabolite profiles revealed that carbon and nitrogen metabolism differed significantly between sunlight and artificial light conditions. The variability of sunlight within and between days could be a factor underlying these differences. Pairwise comparisons of the artificial light sources (fluorescent versus LED) or the light profiles (constant versus sinusoidal) showed much smaller differences. The data indicate that energy-efficient LED lighting is an acceptable alternative to fluorescent lights, but results obtained from plants grown with either type of artificial lighting might not be representative of natural conditions.},
  language  = {en}
}