@article{ZhangRammingHeinkeetal.2019, author = {Zhang, Yunming and Ramming, Anna and Heinke, Lisa and Altschmied, Lothar and Slotkin, R. Keith and Becker, J{\"o}rg D. and Kappel, Christian and Lenhard, Michael}, title = {The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development}, series = {The plant journal}, volume = {99}, journal = {The plant journal}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.14348}, pages = {655 -- 672}, year = {2019}, abstract = {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.}, 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} } @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} } @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{UdDinRaufGhafooretal.2016, author = {Ud-Din, Aziz and Rauf, Mamoona and Ghafoor, S. and Khattak, M. N. K. and Hameed, M. W. and Shah, H. and Jan, S. and Muhammad, K. and Rehman, A. and Inamullah,}, title = {Efficient use of artificial micro-RNA to downregulate the expression of genes at the post-transcriptional level in Arabidopsis thaliana}, series = {Genetics and molecular research}, volume = {15}, journal = {Genetics and molecular research}, publisher = {FUNPEC}, address = {Ribeirao Preto}, issn = {1676-5680}, doi = {10.4238/gmr.15027439}, pages = {11}, year = {2016}, abstract = {Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative realtime polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant.}, 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{TejosRodriguezFurlanAdamowskietal.2018, author = {Tejos, Ricardo and Rodriguez-Furlan, Cecilia and Adamowski, Maciej and Sauer, Michael and Norambuena, Lorena and Friml, Jiri}, title = {PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana}, series = {Journal of cell science}, volume = {131}, journal = {Journal of cell science}, number = {2}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0021-9533}, doi = {10.1242/jcs.204198}, pages = {10}, year = {2018}, abstract = {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.}, language = {en} } @article{SmirnovaFernieSpahnetal.2017, author = {Smirnova, Julia and Fernie, Alisdair R. and Spahn, Christian M. T. and Steup, Martin}, title = {Photometric assay of maltose and maltose-forming enzyme activity by using 4-alpha-glucanotransferase (DPE2) from higher plants}, series = {Analytical biochemistry : methods in the biological sciences}, volume = {532}, journal = {Analytical biochemistry : methods in the biological sciences}, publisher = {Elsevier}, address = {San Diego}, issn = {0003-2697}, doi = {10.1016/j.ab.2017.05.026}, pages = {72 -- 82}, year = {2017}, abstract = {Maltose frequently occurs as intermediate of the central carbon metabolism of prokaryotic and eukaryotic cells. Various mutants possess elevated maltose levels. Maltose exists as two anomers, (alpha- and beta-form) which are rapidly interconverted without requiring enzyme-mediated catalysis. As maltose is often abundant together with other oligoglucans, selective quantification is essential. In this communication, we present a photometric maltose assay using 4-alpha-glucanotransferase (AtDPE2) from Arabidopsis thaliana. Under in vitro conditions, AtDPE2 utilizes maltose as glucosyl donor and glycogen as acceptor releasing the other hexosyl unit as free glucose which is photometrically quantified following enzymatic phosphorylation and oxidation. Under the conditions used, DPE2 does not noticeably react with other di- or oligosaccharides. Selectivity compares favorably with that of maltase frequently used in maltose assays. Reducing end interconversion of the two maltose anomers is in rapid equilibrium and, therefore, the novel assay measures total maltose contents. Furthermore, an AtDPE2-based continuous photometric assay is presented which allows to quantify beta-amylase activity and was found to be superior to a conventional test. Finally, the AtDPE2-based maltose assay was used to quantify leaf maltose contents of both Arabidopsis wild type and AtDPE2-deficient plants throughout the light-dark cycle. These data are presented together with assimilatory starch levels. (C) 2017 Published by Elsevier Inc.}, language = {en} } @misc{SharmaDreyerRiedelsberger2013, author = {Sharma, Tripti and Dreyer, Ingo and Riedelsberger, Janin}, title = {The role of K+ channels in uptake and redistribution of potassium in the model plant Arabidopsis thaliana}, series = {Frontiers in plant science}, volume = {4}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2013.00224}, pages = {16}, year = {2013}, abstract = {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.}, language = {en} } @article{SchwarteWegnerHavensteinetal.2015, author = {Schwarte, Sandra and Wegner, Fanny and Havenstein, Katja and Groth, Detlef and Steup, Martin and Tiedemann, Ralph}, title = {Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana}, series = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, volume = {87}, journal = {Plant molecular biology : an international journal of fundamental research and genetic engineering}, number = {4-5}, publisher = {Springer}, address = {Dordrecht}, issn = {0167-4412}, doi = {10.1007/s11103-015-0293-2}, pages = {489 -- 519}, year = {2015}, abstract = {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.}, language = {en} }