@article{KuekenGennermannNikoloski2020, author = {K{\"u}ken, Anika and Gennermann, Kristin and Nikoloski, Zoran}, title = {Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana}, series = {The plant journal}, volume = {103}, journal = {The plant journal}, number = {6}, publisher = {Wiley}, address = {Oxford}, issn = {0960-7412}, doi = {10.1111/tpj.14890}, pages = {2168 -- 2177}, year = {2020}, abstract = {Availability of plant-specific enzyme kinetic data is scarce, limiting the predictive power of metabolic models and precluding identification of genetic factors of enzyme properties. Enzyme kinetic data are measuredin vitro, often under non-physiological conditions, and conclusions elicited from modeling warrant caution. Here we estimate maximalin vivocatalytic rates for 168 plant enzymes, including photosystems I and II, cytochrome-b6f complex, ATP-citrate synthase, sucrose-phosphate synthase as well as enzymes from amino acid synthesis with previously undocumented enzyme kinetic data in BRENDA. The estimations are obtained by integrating condition-specific quantitative proteomics data, maximal rates of selected enzymes, growth measurements fromArabidopsis thalianarosette with and fluxes through canonical pathways in a constraint-based model of leaf metabolism. In comparison to findings inEscherichia coli, we demonstrate weaker concordance between the plant-specificin vitroandin vivoenzyme catalytic rates due to a low degree of enzyme saturation. This is supported by the finding that concentrations of nicotinamide adenine dinucleotide (phosphate), adenosine triphosphate and uridine triphosphate, calculated based on our maximalin vivocatalytic rates, and available quantitative metabolomics data are below reportedKMvalues and, therefore, indicate undersaturation of respective enzymes. Our findings show that genome-wide profiling of enzyme kinetic properties is feasible in plants, paving the way for understanding resource allocation.}, language = {en} } @article{ThirumalaikumarGorkaSchulzetal.2020, author = {Thirumalaikumar, Venkatesh P. and Gorka, Michal and Schulz, Karina and Masclaux-Daubresse, Celine and Sampathkumar, Arun and Skirycz, Aleksandra and Vierstra, Richard D. and Balazadeh, Salma}, title = {Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1}, series = {Autophagy}, volume = {17}, journal = {Autophagy}, number = {9}, publisher = {Taylor \& Francis}, address = {Abingdon}, issn = {1554-8635}, doi = {10.1080/15548627.2020.1820778}, pages = {2184 -- 2199}, year = {2020}, abstract = {In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS.}, 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} } @article{WangLiMaetal.2021, author = {Wang, Meng and Li, Panpan and Ma, Yao and Nie, Xiang and Grebe, Markus and Men, Shuzhen}, title = {Membrane sterol composition in Arabidopsis thaliana affects root elongation via auxin biosynthesis}, series = {International journal of molecular sciences}, volume = {22}, journal = {International journal of molecular sciences}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms22010437}, pages = {20}, year = {2021}, abstract = {Plant membrane sterol composition has been reported to affect growth and gravitropism via polar auxin transport and auxin signaling. However, as to whether sterols influence auxin biosynthesis has received little attention. Here, by using the sterol biosynthesis mutant cyclopropylsterol isomerase1-1 (cpi1-1) and sterol application, we reveal that cycloeucalenol, a CPI1 substrate, and sitosterol, an end-product of sterol biosynthesis, antagonistically affect auxin biosynthesis. The short root phenotype of cpi1-1 was associated with a markedly enhanced auxin response in the root tip. Both were neither suppressed by mutations in polar auxin transport (PAT) proteins nor by treatment with a PAT inhibitor and responded to an auxin signaling inhibitor. However, expression of several auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) was upregulated in cpi1-1. Functionally, TAA1 mutation reduced the auxin response in cpi1-1 and partially rescued its short root phenotype. In support of this genetic evidence, application of cycloeucalenol upregulated expression of the auxin responsive reporter DR5:GUS (beta-glucuronidase) and of several auxin biosynthesis genes, while sitosterol repressed their expression. Hence, our combined genetic, pharmacological, and sterol application studies reveal a hitherto unexplored sterol-dependent modulation of auxin biosynthesis during Arabidopsis root elongation.}, language = {en} } @article{LiuLiFettke2021, author = {Liu, Qingting and Li, Xiaoping and Fettke, J{\"o}rg}, title = {Starch granules in Arabidopsis thaliana mesophyll and guard cells show similar morphology but differences in size and number}, series = {International journal of molecular sciences}, volume = {22}, journal = {International journal of molecular sciences}, number = {11}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms22115666}, pages = {11}, year = {2021}, abstract = {Transitory starch granules result from complex carbon turnover and display specific situations during starch synthesis and degradation. The fundamental mechanisms that specify starch granule characteristics, such as granule size, morphology, and the number per chloroplast, are largely unknown. However, transitory starch is found in the various cells of the leaves of Arabidopsis thaliana, but comparative analyses are lacking. Here, we adopted a fast method of laser confocal scanning microscopy to analyze the starch granules in a series of Arabidopsis mutants with altered starch metabolism. This allowed us to separately analyze the starch particles in the mesophyll and in guard cells. In all mutants, the guard cells were always found to contain more but smaller plastidial starch granules than mesophyll cells. The morphological properties of the starch granules, however, were indiscernible or identical in both types of leaf cells.}, language = {en} } @article{LiuZhouFettke2021, author = {Liu, Qingting and Zhou, Yuan and Fettke, J{\"o}rg}, title = {Starch granule size and morphology of Arabidopsis thaliana starch-related mutants analyzed during diurnal rhythm and development}, series = {Molecules : a journal of synthetic chemistry and natural product chemistry / Molecular Diversity Preservation International}, volume = {26}, journal = {Molecules : a journal of synthetic chemistry and natural product chemistry / Molecular Diversity Preservation International}, edition = {19}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {1420-3049}, doi = {10.3390/molecules26195859}, pages = {1 -- 9}, year = {2021}, abstract = {Transitory starch plays a central role in the life cycle of plants. Many aspects of this important metabolism remain unknown; however, starch granules provide insight into this persistent metabolic process. Therefore, monitoring alterations in starch granules with high temporal resolution provides one significant avenue to improve understanding. Here, a previously established method that combines LCSM and safranin-O staining for in vivo imaging of transitory starch granules in leaves of Arabidopsis thaliana was employed to demonstrate, for the first time, the alterations in starch granule size and morphology that occur both throughout the day and during leaf aging. Several starch-related mutants were included, which revealed differences among the generated granules. In ptst2 and sex1-8, the starch granules in old leaves were much larger than those in young leaves; however, the typical flattened discoid morphology was maintained. In ss4 and dpe2/phs1/ss4, the morphology of starch granules in young leaves was altered, with a more rounded shape observed. With leaf development, the starch granules became spherical exclusively in dpe2/phs1/ss4. Thus, the presented data provide new insights to contribute to the understanding of starch granule morphogenesis.}, language = {en} } @article{SedaghatmehrThirumalaikumarKamranfaretal.2021, author = {Sedaghatmehr, Mastoureh and Thirumalaikumar, Venkatesh P. and Kamranfar, Iman and Schulz, Karina and M{\"u}ller-R{\"o}ber, Bernd and Sampathkumar, Arun and Balazadeh, Salma}, title = {Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery}, series = {The journal of experimental botany : an official publication of the Society for Experimental Biology and of the Federation of European Societies of Plant Physiology}, volume = {72}, journal = {The journal of experimental botany : an official publication of the Society for Experimental Biology and of the Federation of European Societies of Plant Physiology}, number = {21}, publisher = {Oxford University Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erab304}, pages = {7498 -- 7513}, year = {2021}, abstract = {Moderate and temporary heat stresses prime plants to tolerate, and survive, a subsequent severe heat stress. Such acquired thermotolerance can be maintained for several days under normal growth conditions, and can create a heat stress memory. We recently demonstrated that plastid-localized small heat shock protein 21 ( HSP21) is a key component of heat stress memory in Arabidopsis thaliana. A sustained high abundance of HSP21 during the heat stress recovery phase extends heat stress memory. The level of HSP21 is negatively controlled by plastid-localized metalloprotease FtsH6 during heat stress recovery. Here, we demonstrate that autophagy, a cellular recycling mechanism, exerts additional control over HSP21 degradation. Genetic and chemical disruption of both metalloprotease activity and autophagy trigger superior HSP21 accumulation, thereby improving memory. Furthermore, we provide evidence that autophagy cargo receptor ATG8-INTERACTING PROTEIN1 (ATI1) is associated with heat stress memory. ATI1 bodies co-localize with both autophagosomes and HSP21, and their abundance and transport to the vacuole increase during heat stress recovery. Together, our results provide new insights into the module for control of the regulation of heat stress memory, in which two distinct protein degradation pathways act in concert to degrade HSP21, thereby enabling cells to recover from the heat stress effect at the cost of reducing the heat stress memory.}, language = {en} } @phdthesis{Vyse2022, author = {Vyse, Kora}, title = {Elucidating molecular determinants of the loss of freezing tolerance during deacclimation after cold priming and low temperature memory after triggering}, school = {Universit{\"a}t Potsdam}, pages = {vii, 147}, year = {2022}, abstract = {W{\"a}hrend ihrer Entwicklung m{\"u}ssen sich Pflanzen an Temperaturschwankungen anpassen. Niedrige Temperaturen {\"u}ber dem Gefrierpunkt induzieren in Pflanzen eine K{\"a}lteakklimatisierung und h{\"o}here Frosttoleranz, die sich bei w{\"a}rmeren Temperaturen durch Deakklimatisierung wieder zur{\"u}ckbildet. Der Wechsel zwischen diesen beiden Prozessen ist f{\"u}r Pflanzen unerl{\"a}sslich, um als Reaktion auf unterschiedliche Temperaturbedingungen eine optimale Fitness zu erreichen. Die K{\"a}lteakklimatisierung ist umfassend untersucht worden,{\"u}ber die Regulierung der Deakklimatisierung ist jedoch wenig bekannt. In dieser Arbeit wird der Prozess der Deakklimatisierung auf physiologischer und molekularer Ebene in Arabidopsis thaliana untersucht. Messungen des Elektrolytverlustes w{\"a}hrend der K{\"a}lteakklimatisierung und bis zu vier Tagen nach Deakklimatisierung erm{\"o}glichten die Identifizierung von vier Knockout-Mutanten (hra1, lbd41, mbf1c und jub1), die im Vergleich zum Wildtyp eine langsamere Deakklimatisierungsrate aufwiesen. Eine transkriptomische Studie mit Hilfe von RNA-Sequenzierung von A. thaliana Col-0, jub1 und mbf1c zeigte die Bedeutung der Hemmung von stressreaktiven und Jasmonat-ZIM-Dom{\"a}nen-Genen sowie die Regulierung von Zellwandmodifikationen w{\"a}hrend der Deakklimatisierung. Dar{\"u}ber hinaus zeigten Messungen der Alkoholdehydrogenase Aktivit{\"a}t und der Genexpressions{\"a}nderungen von Hypoxiemarkern w{\"a}hrend der ersten vier Tagen der Deakklimatisierung, dass eine Hypoxie-Reaktion w{\"a}hrend der Deakklimatisierung aktiviert wird. Es wurde gezeigt, dass die epigenetische Regulierung w{\"a}hrend der K{\"a}lteakklimatisierung und der 24-st{\"u}ndigen Deakklimatisierung in A. thaliana eine große Rolle spielt. Dar{\"u}ber hinaus zeigten beide Deakklimatisierungsstudien, dass die fr{\"u}here Hypothese, dass Hitzestress eine Rolle bei der fr{\"u}hen Deakklimatisierung spielen k{\"o}nnte, unwahrscheinlich ist. Eine Reihe von DNA- und Histondemethylasen sowie Histonvarianten wurden w{\"a}hrend der Deakklimatisierung hochreguliert, was auf eine Rolle im pflanzlichen Ged{\"a}chtnis schließen l{\"a}sst. In j{\"u}ngster Zeit haben mehrere Studien gezeigt, dass Pflanzen in der Lage sind, die Erinnerung an einen vorangegangenen K{\"a}ltestress auch nach einer Woche Deakklimatisierung zu bewahren. In dieser Arbeit ergaben Transkriptom- und Metabolomanalysen von Arabidopsis w{\"a}hrend 24 Stunden Priming (K{\"a}lteakklimatisierung) und Triggering (wiederkehrender K{\"a}ltestress nach Deakklimatisierung) eine unikale signifikante und vor{\"u}bergehende Induktion der Transkriptionsfaktoren DREB1D, DREB1E und DREB1F w{\"a}hrend des Triggerings, die zur Feinabstimmung der zweiten K{\"a}ltestressreaktion beitr{\"a}gt. Dar{\"u}ber hinaus wurden Gene, die f{\"u}r Late Embryogenesis Abundant (LEA) und Frostschutzproteine kodieren, sowie Proteine, die reaktive Sauerstoffspezies entgiften, w{\"a}hrend des sp{\"a}ten Triggerings (24 Stunden) st{\"a}rker induziert als nach dem ersten K{\"a}lteimpuls, w{\"a}hrend Xyloglucan- Endotransglucosylase/Hydrolase Gene, deren Produkte f{\"u}r eine Restrukturierung der Zellwand verantwortlich sind, fr{\"u}h auf das Triggering reagierten. Die starke Induktion dieser Gene, sowohl bei der Deakklimatisierung als auch beim Triggering, l{\"a}sst vermuten, dass sie eine wesentliche Rolle bei der Stabilisierung der Zellen w{\"a}hrend des Wachstums und bei der Reaktion auf wiederkehrende Stressbedingungen spielen. Zusammenfassend gibt diese Arbeit neue Einblicke in die Regulierung der Deakklimatisierung und des K{\"a}ltestress-Ged{\"a}chtnisses in A. thaliana und er{\"o}ffnet neue M{\"o}glichkeiten f{\"u}r k{\"u}nftige, gezielte Studien von essentiellen Genen in diesem Prozess.}, language = {en} } @article{RalevskiApeltOlasetal.2022, author = {Ralevski, Alexandra and Apelt, Federico and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Rugarli, Elena I. and Kragler, Friedrich and Horvath, Tamas L.}, title = {Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice}, series = {Cellular and molecular life sciences}, volume = {79}, journal = {Cellular and molecular life sciences}, number = {6}, publisher = {Springer International Publishing AG}, address = {Cham (ZG)}, issn = {1420-682X}, doi = {10.1007/s00018-022-04382-3}, pages = {17}, year = {2022}, abstract = {Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.}, language = {en} } @article{MuntahaLiCompartetal.2022, author = {Muntaha, Sidratul Nur and Li, Xiaoping and Compart, Julia and Apriyanto, Ardha and Fettke, J{\"o}rg}, title = {Carbon pathways during transitory starch degradation in Arabidopsis differentially affect the starch granule number and morphology in the dpe2/phs1 mutant background}, series = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, volume = {180}, journal = {Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology}, publisher = {Elsevier}, address = {Paris}, issn = {0981-9428}, doi = {10.1016/j.plaphy.2022.03.033}, pages = {35 -- 41}, year = {2022}, abstract = {The Arabidopsis knockout mutant lacking both the cytosolic disproportionating enzyme 2 (DPE2) and the plastidial phosphorylase (PHS1) had a dwarf-growth phenotype, a reduced and uneven distribution of starch within the plant rosettes, and a lower starch granule number per chloroplast under standard growth conditions. In contrast, a triple mutant impaired in starch degradation by its additional lack of the glucan, water dikinase (GWD) showed improved plant growth, a starch-excess phenotype, and a homogeneous starch distribution. Furthermore, the number of starch granules per chloroplast was increased and was similar to the wild type. We concluded that ongoing starch degradation is mainly responsible for the observed phenotype of dpe2/phs1. Next, we generated two further triple mutants lacking either the phosphoglucan, water dikinase (PWD), or the disproportionating enzyme 1 (DPE1) in the background of the double mutant. Analysis of the starch metabolism revealed that even minor ongoing starch degradation observed in dpe2/phs1/pwd maintained the double mutant phenotype. In contrast, an additional blockage in the glucose pathway of starch breakdown, as in dpe2/phs1/ dpe1, resulted in a nearly starch-free phenotype and massive chloroplast degradation. The characterized mutants were discussed in the context of starch granule formation.}, language = {en} } @article{MatzWangKulshreshthaetal.2022, author = {Matz, Timon W. and Wang, Yang and Kulshreshtha, Ritika and Sampathkumar, Arun and Nikoloski, Zoran}, title = {Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana}, series = {Development : Company of Biologists}, volume = {149}, journal = {Development : Company of Biologists}, number = {16}, publisher = {Company of Biologists}, address = {Cambridge}, issn = {0950-1991}, doi = {10.1242/dev.201024}, pages = {11}, year = {2022}, abstract = {Cell division and the resulting changes to the cell organization affect the shape and functionality of all tissues. Thus, understanding the determinants of the tissue-wide changes imposed by cell division is a key question in developmental biology. Here, we use a network representation of live cell imaging data from shoot apical meristems (SAMs) in Arabidopsis thaliana to predict cell division events and their consequences at the tissue level. We show that a support vector machine classifier based on the SAM network properties is predictive of cell division events, with test accuracy of 76\%, which matches that based on cell size alone. Furthermore, we demonstrate that the combination of topological and biological properties, including cell size, perimeter, distance and shared cell wall between cells, can further boost the prediction accuracy of resulting changes in topology triggered by cell division. Using our classifiers, we demonstrate the importance of microtubule-mediated cell-to-cell growth coordination in influencing tissue-level topology. Together, the results from our network-based analysis demonstrate a feedback mechanism between tissue topology and cell division in A. thaliana SAMs.}, language = {en} } @phdthesis{Mahto2022, author = {Mahto, Harendra}, title = {In vitro analysis of Early Starvation 1 (ESV1) and Like Early Starvation 1 (LESV) on starch degradation with focus on glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD)}, pages = {167}, year = {2022}, abstract = {Starch is an insoluble polyglucan, comprises of two polymers, namely, the branched α-1,4: α-1,6-D-glucan amylopectin and the almost unbranched α-1,4-D-glucan amylose. The growth of all plants is directly dependent on the accumulation of transitory starch during the daytime when photosynthesis takes place and subsequently starch degradation during the night. Starch phosphorylation takes place by starch-related dikinases called α-glucan, water dikinase (GWD), and phosphoglucan, water dikinase (PWD), and is a very important step in starch degradation. The biochemical mechanisms of phosphorylation of starch are not properly understood. Recent studies have found that there are two starch binding proteins namely, Early Starvation1 (ESV1) and Like Early Starvation1 (LESV), which play an important role in starch metabolism. It has been shown that ESV1 and LESV proteins affect the starch phosphorylation activity of GWD and PWD enzymes, which control the rate of degradation of starch granules. In this thesis, various in vitro assays were performed to identify and understand the mechanism of recombinant proteins; ESV1 and LESV on the starch degradation. The starch degradation was performed by phosphorylation enzymes, GWD and PWD separately. In various enzymatic assays, the influence of the ESV1 and LESV on the actions of GWD and PWD on the surfaces of different native starch granules were analysed. Furthermore, ESV1 and LESV have specifically shown influences on the phosphorylation activities of GWD and PWD on the starch granule surfaces in an antagonistic pattern in such a way that, the GWD mediated phosphorylation were significantly reduced while PWD mediated phosphorylation were significantly increased respectively. In another set of experiments, ISA and BAM hydrolyzing enzymes were used to alter the structure of starch, and then determine the effect of both dikinases mediated phosphorylation in the presence of ESV1 and LESV on the altered starch granules surfaces. In these results, significant decreases in both GWD and PWD mediated phosphorylation were observed in all the treatments containing either ESV1 or LESV proteins only or both ESV1 and LESV. It was also found that LESV preferentially binds to both amylose and amylopectin, while ESV1 binds to highly ordered glucans such as maltodextrins and amylopectin, which are crystalline in structure. Both ESV1 or LESV proteins either individually or in combination have shown influence on the activity of GWD and PWD phosphate incorporation into the starch granules via reduction even though at different percentages depending on the sources of starch, therefore it is difficult to distinguish the specific function between them. The biochemical studies have shown that protein-glucan interaction specifically between ESV1 or LESV or in combination with different species of starch granules has very strong surface binding, or it might be possible that both the proteins not only bind to the surface of the starch granules but also have entered deep inside the glucan structure of the starch granules. However, the results also revealed that ESV1 and LESV did not alter the autophosphorylation of the dikinases. Also, the chain length distribution pattern of the released glucan chains after treatment of starch with ISA enzyme was evaluated with respect to the degree of polymerization (DP) of the different starch granules. Capillary electrophoresis was employed to study the effect of LESV and ESV1 on the chain length distribution. In summary, this study confirms that ESV1 and LESV play an important role in organizing and regulating the starch metabolism process. In the later half, studies were performed to monitor whether the metabolism of carbohydrates and partitioning, contribute to the higher salt tolerance of the facultative halophyte Hordeum marinum when compared to glycophyte Hordeum vulgare. Seedlings with the same size from both species were hydroponically grown at 0, 150, and 300 mM of NaCl for 3 weeks. H. marinum maintained a high relative growth rate, which was found concomitant in higher aptitude plants to maintain efficient shoot tissue hydration and integrity of membrane under salt conditions when compared to H. vulgare. Hence, our data suggested that the change in the starch storage, distribution of soluble sugar concentrations between source and sink organs, and also changes in the level of enzymes involved in the starch metabolism was significant to give insights into the importance of carbohydrate metabolism in barley species with regards to the salt tolerance. Although these results are still in their nascent state, it could be vital for other researchers to formulate future studies. The preliminary results which were studies about the carbohydrate metabolism and partitioning in salt responses in the halophyte H. marinum and the glycophyte H. vulgare revealed that salt tolerance in barley species is not due to osmotic adjustments, but due to other reasons that were not explored in the past studies. However, the activity of DPE2 in H. vulgare was not hampered by the presence of NaCl as observed. While Pho1 and Pho2, activities were highly increased in cultivated barley. These findings could be suggestive of a possible role of these enzymes in the responses of carbohydrate metabolism to salinity. When sea and cultivated barley species were compared, it was discovered that the former had more versatility in carbohydrate metabolism and distribution.}, language = {en} } @phdthesis{vonBismarck2023, author = {von Bismarck, Thekla}, title = {The influence of long-term light acclimation on photosynthesis in dynamic light}, school = {Universit{\"a}t Potsdam}, pages = {x, 163}, year = {2023}, abstract = {Photosynthesis converts light into metabolic energy which fuels plant growth. In nature, many factors influence light availability for photosynthesis on different time scales, from shading by leaves within seconds up to seasonal changes over months. Variability of light energy supply for photosynthesis can limit a plant´s biomass accumulation. Plants have evolved multiple strategies to cope with strongly fluctuation light (FL). These range from long-term optimization of leaf morphology and physiology and levels of pigments and proteins in a process called light acclimation, to rapid changes in protein activity within seconds. Therefore, uncovering how plants deal with FL on different time scales may provide key ideas for improving crop yield. Photosynthesis is not an isolated process but tightly integrates with metabolism through mutual regulatory interactions. We thus require mechanistic understanding of how long-term light acclimation shapes both, dynamic photosynthesis and its interactions with downstream metabolism. To approach this, we analyzed the influence of growth light on i) the function of known rapid photosynthesis regulators KEA3 and VCCN1 in dynamic photosynthesis (Chapter 2-3) and ii) the interconnection of photosynthesis with photorespiration (PR; Chapter 4). We approached topic (i) by quantifying the effect of different growth light regimes on photosynthesis and photoprotection by using kea3 and vccn1 mutants. Firstly, we found that, besides photosynthetic capacity, the activities of VCCN1 and KEA3 during a sudden high light phase also correlated with growth light intensity. This finding suggests regulation of both proteins by the capacity of downstream metabolism. Secondly, we showed that KEA3 accelerated photoprotective non-photochemical quenching (NPQ) kinetics in two ways: Directly via downregulating the lumen proton concentration and thereby de-activating pH-dependent NPQ, and indirectly via suppressing accumulation of the photoprotective pigment zeaxanthin. For topic (ii), we analyzed the role of PR, a process which recycles a toxic byproduct of the carbon fixation reactions, in metabolic flexibility in a dynamically changing light environment. For this we employed the mutants hpr1 and ggt1 with a partial block in PR. We characterized the function of PR during light acclimation by tracking molecular and physiological changes of the two mutants. Our data, in contrast to previous reports, disprove a generally stronger physiological relevance of PR under dynamic light conditions. Additionally, the two different mutants showed pronounced and distinct metabolic changes during acclimation to a condition inducing higher photosynthetic activity. This underlines that PR cannot be regarded purely as a cyclic detoxification pathway for 2PG. Instead, PR is highly interconnected with plant metabolism, with GGT1 and HPR1 representing distinct metabolic modulators. In summary, the presented work provides further insight into how energetic and metabolic flexibility is ensured by short-term regulators and PR during long-term light acclimation.}, language = {en} } @article{KappelFriedrichOberkofleretal.2023, author = {Kappel, Christian and Friedrich, Thomas and Oberkofler, Vicky and Jiang, Li and Crawford, Tim and Lenhard, Michael and B{\"a}urle, Isabel}, title = {Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis}, series = {Genome biology : biology for the post-genomic era}, volume = {24}, journal = {Genome biology : biology for the post-genomic era}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {1474-760X}, doi = {10.1186/s13059-023-02970-5}, pages = {23}, year = {2023}, abstract = {Background Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. Results HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. Conclusions Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.}, 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} } @phdthesis{Liu2024, author = {Liu, Qingting}, title = {Regulation of Starch Granule Morphogenesis in Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {124}, year = {2024}, abstract = {Carbohydrates play a vital role in all living organisms; serving as a cornerstone in primary metabolism through the release of energy from their hydrolysis and subsequent re-utilization (Apriyanto et al., 2022). Starch is the principal carbohydrate reserve in plants, providing essential energy for plant growth. Furthermore, starch serves as a significant carbohydrate source in the human diet. Beyond its nutritional value, starch has extensive industrial application associated with many aspects of human society, such as feed, pharmacy, textiles, and the production of biodegradable plastics. Understanding the mechanisms underlying starch metabolism in plants carries multifaceted benefits. Not only does it contribute to increasing crop yield and refining grain quality, but also can improve the efficiency of industrial applications. Starch in plants is categorized into two classes based on their location and function: transitory starch and storage starch. Transitory starch is produced in chloroplasts of autotrophic tissues/organs, such as leaves. It is synthesized during the day and degraded during the night. Storage starch is synthesized in heterotrophic tissues/organs, such as endosperm, roots and tubers, which is utilized for plant reproduction and industrial application in human life. Most studies aiming to comprehend starch metabolism of Arabidopsis thaliana primarily focus on transitory starch. Starch is stored as granular form in chloroplast and amyloplast. The parameters of starch granules, including size, morphology, and quantity per chloroplast serve as indicators of starch metabolism status. However, the understanding of their regulatory mechanism is still incomplete. In this research, I initially employed a simple and adapted method based on laser confocal scanning microscopy (LCSM) to observe size, morphology and quantity of starch granules within chloroplasts in Arabidopsis thaliana in vivo. This method facilitated a rapid and versatile analysis of starch granule parameters across numerous samples. Utilizing this approach, I compared starch granule number per chloroplast between mesophyll cells and guard cells in both wild type plants (Col-0) and several starch related mutants. The results revealed that the granule number is distinct between mesophyll cells and guard cells, even within the same genetic background, suggesting that guard cells operate a unique regulatory mechanism of starch granule number. Subsequently, I redirected my attention toward examining starch morphology. Through microscopy analyses, I observed a gradual alteration in starch granule morphology in certain mutants during leaf aging. Specifically, in mutants such as sex1-8 and dpe2phs1ss4, there was a progressive alteration in starch granule morphology over time. Conversely, in Col-0 and ss4 mutant, these morphological alterations were not evident. This discovery suggests a new perspective to understand the development of starch morphology. Further investigation revealed that mutants lacking either Disproportionating enzyme 2 (DPE2) or MALTOSE-EXCESS 1 (MEX1) exhibited gradual alterations in starch morphology with leaf aging. Notably, the most severe effects on starch morphology occurred in double mutants lacking either DPE2 or MEX1 in conjunction with a lack of starch synthase 4 (SS4). In these mutations, a transformation of the starch granule morphology from the typical discoid morphology to oval and eventually to a spherical shape. To investigate the changes in the internal structure of starch during this alteration, I analyzed the chain length distribution (CLD) of the amylopectin of young, intermediate and old leaves of the mutants. Throughout starch granule development, I found an increased presence of short glucan chains within the granules, particularly evident in dpe2ss4 and mex1ss4 mutants, as well as their parental single mutants. Notably, the single mutant ss4 also showed an affected granule morphology, albeit not influenced by leaf aging.. The CLD pattern of the amylopectin reflects an integrative regulation involving several participants in starch synthesis, including starch synthases (SSs), starch branching/debranching enzymes (SBEs/DBEs). Therefore, I further detected the expression of related genes on transcription level and the enzymatic activity of their respective proteins. Results indicated altered gene expression of several regulators in these mutants, particularly demonstrating dramatic alterations in dpe2 and dpe2ss4 with leaf aging. These changes corresponded with the observed alterations in starch granule morphology. Taken together, I have identified and characterized a progressive alteration in starch granule morphology primarily resulting from the deficiencies in DPE2 and MEX1. Furthermore, I have associated the CLD pattern with the granule morphogenesis, as well as the gene expression and enzymatic activity of proteins involved in starch synthesis. Unlike SS4, which is implicated in starch initiation, MEX1 and DPE2 are involved into starch degradation. MEX1 is located in chloroplast envelope and DPE2 is situated in the cytosol. Considering the locations and known functions of DPE2/MEX1 and SS4, I infer that there might be two pathways influencing starch morphology: an initiation-affected pathway via SS4 and a degradation-affected pathway via DPE2/MEX1.}, language = {en} }