TY - JOUR A1 - Sharma, Tripti A1 - Dreyer, Ingo A1 - Riedelsberger, Janin T1 - The role of K+ channels in uptake and redistribution of potassium in the model plant Arabidopsis thaliana JF - Frontiers in plant science N2 - Potassium (K+) is inevitable for plant growth and development. It plays a crucial role in the regulation of enzyme activities, in adjusting the electrical membrane potential and the cellular turgor, in regulating cellular homeostasis and in the stabilization of protein synthesis. Uptake of K+ from the soil and its transport to growing organs is essential for a healthy plant development. Uptake and allocation of K+ are performed by K+ channels and transporters belonging to different protein families. In this review we summarize the knowledge on the versatile physiological roles of plant K+ channels and their behavior under stress conditions in the model plant Arabidopsis thaliana. KW - plant potassium channel KW - Shaker KW - TPK KW - K-ir-like KW - Arabidopsis thaliana KW - voltage-dependent KW - voltage-independent Y1 - 2013 U6 - https://doi.org/10.3389/fpls.2013.00224 SN - 1664-462X VL - 4 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Zhang, Yunming A1 - Ramming, Anna A1 - Heinke, Lisa A1 - Altschmied, Lothar A1 - Slotkin, R. Keith A1 - Becker, Jörg D. A1 - Kappel, Christian A1 - Lenhard, Michael T1 - The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development JF - The plant journal N2 - RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast. KW - poly(A) polymerase KW - RNA-directed DNA methylation KW - pollen development KW - siRNAs KW - transposable elements KW - gynoecium development KW - Arabidopsis thaliana Y1 - 2019 U6 - https://doi.org/10.1111/tpj.14348 SN - 0960-7412 SN - 1365-313X VL - 99 IS - 4 SP - 655 EP - 672 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Gonzalez, Wendy A1 - Riedelsberger, Janin A1 - Morales-Navarro, Samuel E. A1 - Caballero, Julio A1 - Alzate-Morales, Jans H. A1 - Gonzalez-Nilo, Fernando D. A1 - Dreyer, Ingo T1 - The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids JF - The biochemical journal N2 - The uptake of potassium ions (K+) accompanied by an acidification of the apoplasm is a prerequisite for stomatal opening. The acidification (approximately 2-2.5 pH units) is perceived by voltage-gated inward potassium channels (K-in) that then can open their pores with lower energy cost. The sensory units for extracellular pH in stomatal K-in channels are proposed to be histidines exposed to the apoplasm. However, in the Arabidopsis thaliana stomatal K-in channel KAT1, mutations in the unique histidine exposed to the solvent (His(267)) do not affect the pH dependency. We demonstrate in the present study that His(267) of the KAT1 channel cannot sense pH changes since the neighbouring residue Phe(266) shifts its pK(a) to undetectable values through a cation-pi interaction. Instead, we show that Glu(240) placed in the extracellular loop between transmembrane segments S5 and S6 is involved in the extracellular acid activation mechanism. Based on structural models we propose that this region may serve as a molecular link between the pH- and the voltage-sensor. Like Glu(240), several other titratable residues could contribute to the pH-sensor of KAT1, interact with each other and even connect such residues far away from the voltage-sensor with the gating machinery of the channel. KW - Arabidopsis thaliana KW - channel protein structure KW - channel protein-proton interaction KW - KAT1 KW - pH regulation KW - potassium chanel Y1 - 2012 U6 - https://doi.org/10.1042/BJ20111498 SN - 0264-6021 VL - 442 IS - 7 SP - 57 EP - 63 PB - Portland Press CY - London ER - TY - THES A1 - von Bismarck, Thekla T1 - The influence of long-term light acclimation on photosynthesis in dynamic light N2 - 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. N2 - Photosynthese wandelt Lichtenergie in metabolische Energie um, welche das Pflanzenwachstum antreibt. In der Natur wird die Verfügbarkeit von Licht von vielerlei Faktoren auf unterschiedlichen Zeitskalen beeinflusst, z. B. von der Beschattung durch Blätter innerhalb von Sekunden bis hin zu jahreszeitlichen Veränderungen über Monate. Fluktuationen in der Lichtenergieverfügbarkeit in der Natur kann die Biomasseakkumulation der Pflanzen limitieren. Pflanzen haben verschiedene Strategien entwickelt, um stark fluktuierendes Licht nutzen zu können. Diese reichen von der langfristigen Optimierung der Blattmorphologie und Physiologie und des Gehalts an Pigmenten und Proteinen in dem Prozess der Lichtakklimatisierung bis hin zu schnellen Veränderungen der Proteinaktivität innerhalb von Sekunden. Daher kann die Aufdeckung der Art und Weise, wie Pflanzen mit FL auf verschiedenen Zeitskalen umgehen, wichtige Ideen zur Verbesserung der Ernteerträge liefern. Die Photosynthese ist kein isolierter Prozess, sondern steht in enger Interaktion mit den nachgeschalteten Stoffwechselwegen. Daher benötigen wir mechanistisches Verständnis, wie Lichtakklimatisierung die dynamische Photosynthese als auch deren Interaktion mit Downstream-Metabolismus moduliert. Dafür haben wir den Einfluss von Lichtakklimatisierung auf i) die Funktion der schnellen Photosyntheseregulatoren KEA3 und VCCN1 in der dynamischen Photosynthese und ii) die flexible Interaktion von Photorespiration mit Photosynthese analysiert. Im ersten Themenkomplex (i) wurden die Auswirkungen verschiedener Wachstumslicht-bedingungen auf Photosynthese und Photoprotektion anhand von kea3- und vccn1-Mutanten quantifiziert. Zum einen konnten wir zeigen, dass neben der photosynthetischen Kapazität auch die Aktivitäten von VCCN1 und KEA3 während eines Hochlichtpulses mit der Wachstumslichtintensität korrelierten. Dies deutet auf eine Regulierung beider Proteine durch die Kapazität des Downstream-Metabolismus hin. Zum anderen beschleunigte KEA3 die Kinetik des photoprotektiven nicht-photochemischen Quenchings (NPQ) auf zweifache Weise: Direkt über die Herabregulierung der lumenalen Protonenkonzentration, was den pH-abhängigen NPQ deaktivierte, und indirekt über die Unterdrückung der Akkumulation des photoprotektiven Pigments Zeaxanthin. Für das zweite Thema (ii) untersuchten wir die Rolle des photorespiratorischen Metabolismus (PR), welcher ein toxisches Nebenprodukt der Kohlenstofffixierungsreaktionen recycelt, in der metabolischen Flexibilität in einer sich dynamisch verändernden Lichtumgebung. Dazu verwendeten wir die Mutanten hpr1 und ggt1 mit teilweise blockiertem PR Flux. Unsere Daten widerlegen, im Gegensatz zu früheren Berichten, eine allgemein größere physiologische Bedeutung von PR unter dynamischen Lichtbedingungen. Die beiden Mutanten zeigten ausgeprägte und distinkte metabolische Veränderungen während der Akklimatisierung an eine Bedingung mit höherer photosynthetischer Aktivität. Dies zeigt, dass PR nicht ausschließlich als zyklischer Entgiftungsweg für 2PG angesehen werden kann. Vielmehr ist PR tief in den pflanzlichen Stoffwechsel eingebettet, wobei GGT1 und HPR1 als distinkte Stellschrauben des Downstream-Metabolismus agieren. Zusammenfassend liefert die vorliegende Arbeit weitere Erkenntnisse darüber, wie die energetische und metabolische Flexibilität durch kurzfristige Regulatoren und den photorespiratorischen Metabolismus während der langfristigen Lichtakklimatisierung gewährleistet wird. KW - photosynthesis KW - fluctuating light KW - Arabidopsis thaliana KW - Photosynthese KW - fluktuierendes Licht Y1 - 2023 ER - TY - JOUR A1 - Lisso, Janina A1 - Altmann, Thomas A1 - Müssig, Carsten T1 - The AtNFXL1 gene encodes a NF-X1 type zinc finger protein required for growth under salt stress JF - FEBS letters : the journal for rapid publication of short reports in molecular biosciences N2 - The human NF-X1 protein and homologous proteins in eukaryotes represent a class of transcription factors which are characterised. by NF-X1 type zinc finger motifs. The Arabidopsis genome encodes two NF-X1 homologs, which we termed AtNFXL1 and AtNFXL2. Growth and survival was impaired in atnfxl1 knock-out mutants and AtNFXL1-antisense plants under salt stress in comparison to wild-type plants. In contrast, 35S: :AtNFXL1 plants showed higher survival rates. The AtNFXL2 protein potentially plays an antagonistic role. The Arabidopsis NF-X1 type zinc finger proteins likely are part of regulatory mechanisms, which protect major processes such as photosynthesis. KW - Arabidopsis thaliana KW - NF-X1 KW - salt stress Y1 - 2006 U6 - https://doi.org/10.1016/j.febslet.2006.07.079 SN - 0014-5793 VL - 580 IS - 22 SP - 4851 EP - 4856 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Liu, Qingting A1 - Li, Xiaoping A1 - Fettke, Jörg T1 - Starch granules in Arabidopsis thaliana mesophyll and guard cells show similar morphology but differences in size and number JF - International journal of molecular sciences N2 - 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. KW - starch granules KW - starch granule number per chloroplast KW - starch morphology KW - mesophyll cell KW - guard cell KW - LCSM KW - Arabidopsis thaliana KW - starch granule initiation KW - starch metabolism Y1 - 2021 U6 - https://doi.org/10.3390/ijms22115666 SN - 1422-0067 SN - 1661-6596 VL - 22 IS - 11 PB - Molecular Diversity Preservation International CY - Basel ER - TY - JOUR A1 - Liu, Qingting A1 - Zhou, Yuan A1 - Fettke, Jörg T1 - Starch granule size and morphology of Arabidopsis thaliana starch-related mutants analyzed during diurnal rhythm and development JF - Molecules : a journal of synthetic chemistry and natural product chemistry / Molecular Diversity Preservation International N2 - 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. KW - starch metabolism KW - starch granule KW - starch granule size KW - starch granule morphology KW - LCSM KW - Arabidopsis thaliana Y1 - 2021 U6 - https://doi.org/10.3390/molecules26195859 SN - 1420-3049 VL - 26 SP - 1 EP - 9 PB - MDPI CY - Basel, Schweiz ET - 19 ER - TY - JOUR A1 - Merida, Angel A1 - Fettke, Jörg T1 - Starch granule initiation in Arabidopsis thaliana chloroplasts JF - The plant journal N2 - 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. KW - starch granules KW - starch metabolism KW - starch granule initiation KW - starch KW - granule number per chloroplast KW - starch morphology KW - Arabidopsis thaliana Y1 - 2021 U6 - https://doi.org/10.1111/tpj.15359 SN - 0960-7412 SN - 1365-313X VL - 107 IS - 3 SP - 688 EP - 697 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Schwarte, Sandra A1 - Wegner, Fanny A1 - Havenstein, Katja A1 - Groth, Detlef A1 - Steup, Martin A1 - Tiedemann, Ralph T1 - Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana JF - Plant molecular biology : an international journal of fundamental research and genetic engineering N2 - Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts. KW - Arabidopsis thaliana KW - Divergent evolution KW - Intraspecific genetic variation KW - Positive selection KW - Starch metabolizing enzymes KW - Transcript levels Y1 - 2015 U6 - https://doi.org/10.1007/s11103-015-0293-2 SN - 0167-4412 SN - 1573-5028 VL - 87 IS - 4-5 SP - 489 EP - 519 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Thirumalaikumar, Venkatesh P. A1 - Gorka, Michal A1 - Schulz, Karina A1 - Masclaux-Daubresse, Celine A1 - Sampathkumar, Arun A1 - Skirycz, Aleksandra A1 - Vierstra, Richard D. A1 - Balazadeh, Salma T1 - Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1 JF - Autophagy N2 - 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. KW - Arabidopsis thaliana KW - heat stress KW - HSFA2 KW - HSP90.1 KW - NBR1 KW - ROF1 KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2020 U6 - https://doi.org/10.1080/15548627.2020.1820778 SN - 1554-8635 VL - 17 IS - 9 SP - 2184 EP - 2199 PB - Taylor & Francis CY - Abingdon ER - TY - JOUR A1 - Parlitz, Steffi A1 - Kunze, Reinhard A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Regulation of photosynthesis and transcription factor expression by leaf shading and re-illumination in Arabidopsis thaliana leaves JF - Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants N2 - Leaf senescence of annual plants is a genetically programmed developmental phase. The onset of leaf senescence is however not exclusively determined by tissue age but is modulated by various environmental factors. Shading of individual attached leaves evokes dark-induced senescence. The initiation and progression of dark-induced senescence depend on the plant and the age of the affected leaf, however. In several plant species dark-induced senescence is fully reversible upon re-illumination and the leaves can regreen, but the regreening ability depends on the duration of dark incubation. We studied the ability of Arabidopsis thaliana leaves to regreen after dark-incubation with the aim to identify transcription factors (TFs) that are involved in the regulation of early dark-induced senescence and regreening. Two days shading of individual attached leaves triggers the transition into a pre-senescence state from which the leaves can largely recover. Longer periods of darkness result in irreversible senescence. Large scale qRT-PCR analysis of 1872 TF genes revealed that 649 of them are regulated in leaves during normal development, upon shading or re-illumination. Leaf shading triggered upregulation of 150 TF genes, some of which are involved in controlling senescence. Of those, 39 TF genes were upregulated after two days in the dark and regained pre-shading expression level after two days of re-illumination. Furthermore, a larger number of 422 TF genes were down regulated upon shading. In TF gene clusters with different expression patterns certain TF families are over-represented. KW - Arabidopsis thaliana KW - Dark-induced senescence KW - Expression profiling KW - Regreening KW - Transcription factor Y1 - 2011 U6 - https://doi.org/10.1016/j.jplph.2011.02.001 SN - 0176-1617 VL - 168 IS - 12 SP - 1311 EP - 1319 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Poxson, David J. A1 - Karady, Michal A1 - Gabrielsson, Roger A1 - Alkattan, Aziz Y. A1 - Gustavsson, Anna A1 - Doyle, Siamsa M. A1 - Robert, Stephanie A1 - Ljung, Karin A1 - Grebe, Markus A1 - Simon, Daniel T. A1 - Berggren, Magnus T1 - Regulating plant physiology with organic electronics JF - Proceedings of the National Academy of Sciences of the United States of America N2 - The organic electronic ion pump (OEIP) provides flow-free and accurate delivery of small signaling compounds at high spatio-temporal resolution. To date, the application of OEIPs has been limited to delivery of nonaromatic molecules to mammalian systems, particularly for neuroscience applications. However, many long-standing questions in plant biology remain unanswered due to a lack of technology that precisely delivers plant hormones, based on cyclic alkanes or aromatic structures, to regulate plant physiology. Here, we report the employment of OEIPs for the delivery of the plant hormone auxin to induce differential concentration gradients and modulate plant physiology. We fabricated OEIP devices based on a synthesized dendritic polyelectrolyte that enables electrophoretic transport of aromatic substances. Delivery of auxin to transgenic Arabidopsis thaliana seedlings in vivo was monitored in real time via dynamic fluorescent auxin-response reporters and induced physiological responses in roots. Our results provide a starting point for technologies enabling direct, rapid, and dynamic electronic interaction with the biochemical regulation systems of plants. KW - auxin KW - Arabidopsis thaliana KW - dendritic polymer KW - bioelectronics KW - polyelectrolyte Y1 - 2017 U6 - https://doi.org/10.1073/pnas.1617758114 SN - 0027-8424 VL - 114 SP - 4597 EP - 4602 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Pandey, Prashant K. A1 - Yu, Jing A1 - Omranian, Nooshin A1 - Alseekh, Saleh A1 - Vaid, Neha A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran A1 - Laitinen, Roosa A. E. T1 - Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations JF - Plant Direct N2 - Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution. KW - Arabidopsis thaliana KW - natural variation KW - nitrogen availability KW - photorespiration KW - plasticity Y1 - 2019 U6 - https://doi.org/10.1002/pld3.186 SN - 2475-4455 VL - 3 IS - 11 PB - John Wiley & sonst LTD CY - Chichester ER - TY - JOUR A1 - Naseri, Gita A1 - Balazadeh, Salma A1 - Machens, Fabian A1 - Kamranfar, Iman A1 - Messerschmidt, Katrin A1 - Müller-Röber, Bernd T1 - Plant-Derived Transcription Factors for Orthologous Regulation of Gene Expression in the Yeast Saccharomyces cerevisiae JF - ACS synthetic biology N2 - Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects for which a tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harboring cognate cis regulatory motifs driving a yEGFP reporter. Transcriptional output of the different driver/reporter combinations varied over a wide spectrum, with EDLL being a considerably stronger transcription activation domain in yeast than the GAL4 activation domain, in particular when fused to Arabidopsis NAC TFs. Notably, the strength of several NAC-EDLL fusions exceeded that of the strong yeast TDH3 promoter by 6- to 10-fold. We furthermore show that plant TFs can be used to build regulatory systems encoded by centromeric or episomal plasmids. Our library of TF-DNA binding site combinations offers an excellent tool for diverse synthetic biology applications in yeast. KW - Arabidopsis thaliana KW - artificial transcription factor KW - NAC transcription factor KW - synthetic biology KW - plant Y1 - 2017 U6 - https://doi.org/10.1021/acssynbio.7b00094 SN - 2161-5063 VL - 6 SP - 1742 EP - 1756 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Ralevski, Alexandra A1 - Apelt, Federico A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Rugarli, Elena I. A1 - Kragler, Friedrich A1 - Horvath, Tamas L. T1 - Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice JF - Cellular and molecular life sciences N2 - 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. KW - Arabidopsis thaliana KW - Mitochondria KW - FMT KW - Hyponasty KW - Mice KW - CLUH; KW - Locomotion Y1 - 2022 U6 - https://doi.org/10.1007/s00018-022-04382-3 SN - 1420-682X SN - 1420-9071 VL - 79 IS - 6 PB - Springer International Publishing AG CY - Cham (ZG) ER - TY - JOUR A1 - Apelt, Federico A1 - Breuer, David A1 - Nikoloski, Zoran A1 - Stitt, Mark A1 - Kragler, Friedrich T1 - Phytotyping(4D): a light-field imaging system for non-invasive and accurate monitoring of spatio-temporal plant growth JF - The plant journal N2 - Integrative studies of plant growth require spatially and temporally resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, termed hyponasty. To solve this problem, Phytotyping(4D) uses a light-field camera that simultaneously provides a focus image and a depth image, which contains distance information about the object surface. Our automated pipeline segments the focus images, integrates depth information to reconstruct the three-dimensional architecture, and analyses time series to provide information about the relative expansion rate, the timing of leaf appearance, hyponastic movement, and shape for individual leaves and the whole rosette. Phytotyping(4D) was calibrated and validated using discs of known sizes, and plants tilted at various orientations. Information from this analysis was integrated into the pipeline to allow error assessment during routine operation. To illustrate the utility of Phytotyping(4D), we compare diurnal changes in Arabidopsis thaliana wild-type Col-0 and the starchless pgm mutant. Compared to Col-0, pgm showed very low relative expansion rate in the second half of the night, a transiently increased relative expansion rate at the onset of light period, and smaller hyponastic movement including delayed movement after dusk, both at the level of the rosette and individual leaves. Our study introduces light-field camera systems as a tool to accurately measure morphological and growth-related features in plants. Significance Statement Phytotyping(4D) is a non-invasive and accurate imaging system that combines a 3D light-field camera with an automated pipeline, which provides validated measurements of growth, movement, and other morphological features at the rosette and single-leaf level. In a case study in which we investigated the link between starch and growth, we demonstrated that Phytotyping(4D) is a key step towards bridging the gap between phenotypic observations and the rich genetic and metabolic knowledge. KW - plant growth KW - hyponasty KW - 3D imaging KW - light-field camera KW - Arabidopsis thaliana KW - pgm KW - technical advance Y1 - 2015 U6 - https://doi.org/10.1111/tpj.12833 SN - 0960-7412 SN - 1365-313X VL - 82 IS - 4 SP - 693 EP - 706 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Smirnova, Julia A1 - Fernie, Alisdair R. A1 - Spahn, Christian M. T. A1 - Steup, Martin T1 - Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants JF - Analytical biochemistry : methods in the biological sciences N2 - 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. KW - Arabidopsis thaliana KW - beta-amylase assay KW - Disproportionating isozyme 2 (DPE2) dpe2-deficient plants KW - Maltose assay KW - Leaf maltose content Y1 - 2017 U6 - https://doi.org/10.1016/j.ab.2017.05.026 SN - 0003-2697 SN - 1096-0309 VL - 532 SP - 72 EP - 82 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Mahlow, Sebastian A1 - Hejazi, Mahdi A1 - Kuhnert, Franziska A1 - Garz, Andreas A1 - Brust, Henrike A1 - Baumann, Otto A1 - Fettke, Jörg T1 - Phosphorylation of transitory starch by -glucan, water dikinase during starch turnover affects the surface properties and morphology of starch granules JF - New phytologist : international journal of plant science N2 - Glucan, water dikinase (GWD) is a key enzyme of starch metabolism but the physico-chemical properties of starches isolated from GWD-deficient plants and their implications for starch metabolism have so far not been described. Transgenic Arabidopsis thaliana plants with reduced or no GWD activity were used to investigate the properties of starch granules. In addition, using various in vitro assays, the action of recombinant GWD, -amylase, isoamylase and starch synthase 1 on the surface of native starch granules was analysed. The internal structure of granules isolated from GWD mutant plants is unaffected, as thermal stability, allomorph, chain length distribution and density of starch granules were similar to wild-type. However, short glucan chain residues located at the granule surface dominate in starches of transgenic plants and impede GWD activity. A similarly reduced rate of phosphorylation by GWD was also observed in potato tuber starch fractions that differ in the proportion of accessible glucan chain residues at the granule surface. A model is proposed to explain the characteristic morphology of starch granules observed in GWD transgenic plants. The model postulates that the occupancy rate of single glucan chains at the granule surface limits accessibility to starch-related enzymes. KW - Arabidopsis thaliana KW - glucan KW - water dikinase (GWD) KW - sex1-8 KW - starch granule surface KW - starch phosphorylation Y1 - 2014 U6 - https://doi.org/10.1111/nph.12801 SN - 0028-646X SN - 1469-8137 VL - 203 IS - 2 SP - 495 EP - 507 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Tejos, Ricardo A1 - Rodriguez-Furlan, Cecilia A1 - Adamowski, Maciej A1 - Sauer, Michael A1 - Norambuena, Lorena A1 - Friml, Jiri T1 - PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana JF - Journal of cell science N2 - Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis. KW - PATELLIN KW - Auxin KW - Arabidopsis thaliana KW - Auxin transport KW - Canalization Y1 - 2018 U6 - https://doi.org/10.1242/jcs.204198 SN - 0021-9533 SN - 1477-9137 VL - 131 IS - 2 PB - Company of Biologists Limited CY - Cambridge ER - TY - JOUR A1 - Matallana-Ramirez, Lilian P. A1 - Rauf, Mamoona A1 - Farage-Barhom, Sarit A1 - Dortay, Hakan A1 - Xue, Gang-Ping A1 - Droege-Laser, Wolfgang A1 - Lers, Amnon A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis JF - Molecular plant N2 - The NAC transcription factor ORE1 is a key regulator of senescence in Arabidopsis thaliana. Here, we demonstrate that senescence-induced and cell death-associated BIFUNCTIONAL NUCLEASE1 (BFN1) is a direct downstream target of ORE1, revealing a previously unknown regulatory cascade.Senescence is a highly regulated process that involves the action of a large number of transcription factors. The NAC transcription factor ORE1 (ANAC092) has recently been shown to play a critical role in positively controlling senescence in Arabidopsis thaliana; however, no direct target gene through which it exerts its molecular function has been identified previously. Here, we report that BIFUNCTIONAL NUCLEASE1 (BFN1), a well-known senescence-enhanced gene, is directly regulated by ORE1. We detected elevated expression of BFN1 already 2 h after induction of ORE1 in estradiol-inducible ORE1 overexpression lines and 6 h after transfection of Arabidopsis mesophyll cell protoplasts with a 35S:ORE1 construct. ORE1 and BFN1 expression patterns largely overlap, as shown by promoterreporter gene (GUS) fusions, while BFN1 expression in senescent leaves and the abscission zones of maturing flower organs was virtually absent in ore1 mutant background. In vitro binding site assays revealed a bipartite ORE1 binding site, similar to that of ORS1, a paralog of ORE1. A bipartite ORE1 binding site was identified in the BFN1 promoter; mutating the cis-element within the context of the full-length BFN1 promoter drastically reduced ORE1-mediated transactivation capacity in transiently transfected Arabidopsis mesophyll cell protoplasts. Furthermore, chromatin immunoprecipitation (ChIP) demonstrates in vivo binding of ORE1 to the BFN1 promoter. We also demonstrate binding of ORE1 in vivo to the promoters of two other senescence-associated genes, namely SAG29/SWEET15 and SINA1, supporting the central role of ORE1 during senescence. KW - Arabidopsis thaliana KW - senescence KW - transcription factor KW - ORE1 KW - BFN1 KW - promoter Y1 - 2013 U6 - https://doi.org/10.1093/mp/sst012 SN - 1674-2052 VL - 6 IS - 5 SP - 1438 EP - 1452 PB - Oxford Univ. Press CY - Oxford ER -