TY - JOUR A1 - García-Camacho, Raúl A1 - Metz, Johannes A1 - Bilton, Mark C. A1 - Tielboerger, Katja T1 - Phylogenetic structure of annual plant communities along an aridity gradient BT - Interacting effects of habitat filtering and shifting plant-plant interactions JF - Israel Journal of Plant Sciences N2 - The phylogenetic structure of communities (PSC) reveals how evolutionary history affects community assembly processes. However, there are important knowledge gaps on PSC patterns for annual communities and there is a need for studies along environmental gradients in dry ecosystems where several processes shape PSC. Here, we investigated the PSC of annual plants along an aridity gradient in Israel, including eight years, two spatial scales, the effects of shrubs on understory, and the phylogenetic signal of important traits. Increasing drought stress led to overdispersed PSC at the drier end of the gradient, indicating that species were less related than expected by chance. This was supported at a smaller spatial scale, where within the drier sites, communities in open- more arid- habitats were more overdispersed than those under nurse shrubs. Interestingly, some key traits related to drought resistance were not conserved in the phylogeny. Together, our findings suggested that while habitat filtering selected for drought resistance strategies, these strategies evolved independently along multiple contrasting evolutionary lineages. Our comprehensive PSC study provides strong evidence for the interacting effects of habitat filtering and plant- plant interactions, particularly highlighting that the conservative evolution of traits should not be assumed in future interpretations of PSC patterns. KW - Annuals KW - aridity gradient KW - community assembly rules KW - community phylogenetics KW - stress-gradient hypothesis KW - trait phylogenetic conservatism Y1 - 2017 U6 - https://doi.org/10.1080/07929978.2017.1288477 SN - 0792-9978 SN - 2223-8980 VL - 64 IS - 1-2 SP - 122 EP - 134 PB - Taylor & Francis CY - London ER - TY - JOUR A1 - Trindade, Inês T1 - License to flower BT - LEAFY has pioneer activity JF - Molecular plant Y1 - 2021 U6 - https://doi.org/10.1016/j.molp.2021.04.007 SN - 1674-2052 SN - 1752-9867 VL - 14 IS - 5 SP - 719 EP - 720 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Heinze, Johannes T1 - The impact of soil microbiota on plant species performance and diversity in semi-natural grasslands Y1 - 2016 ER - TY - GEN A1 - Köchy, Martin A1 - Tielbörger, Katja T1 - Hydrothermal time model of germination : parameters for 36 Mediterranean annual species based on a simplified approach N2 - Germination rates and germination fractions of seeds can be predicted well by the hydrothermal time (HTT) model. Its four parameters hydrothermal time, minimum soil temperature, minimum soil moisture, and variation of minimum soil moisture, however, must be determined by lengthy germination experiments at combinations of several levels of soil temperature and moisture. For some applications of the HTT model it is more important to have approximate estimates for many species rather than exact values for only a few species. We suggest that minimum temperature and variation of minimum moisture can be estimated from literature data and expert knowledge. This allows to derive hydrothermal time and minimum moisture from existing data from germination experiments with one level of temperature and moisture. We applied our approach to a germination experiment comparing germination fractions of wild annual species along an aridity gradient in Israel. Using this simplified approach we estimated hydrothermal time and minimum moisture of 36 species. Comparison with exact data for three species shows that our method is a simple but effective method for obtaining parameters for the HTT model. Hydrothermal time and minimum moisture supposedly indicate climate related germination strategies. We tested whether these two parameters varied with the climate at the site where the seeds had been collected. We found no consistent variation with climate across species, suggesting that variation is more strongly controlled by site-specific factors. N2 - Keimungsgeschwindigkeit und Anteil gekeimter Samen lassen sich gut mit dem Hydrothermalzeit-Modell bestimmen. Dessen vier Parameter Hydrothermalzeit, Mindesttemperatur, Mindestbodenfeuchte und Streuung der Mindestbodenfeuchte müssen jedoch durch aufwendige Keimungsversuche bei Kombinationen von mehreren Temperatur- und Feuchtigkeitsstufen bestimmt werden. Für manche Anwendungen des Hydrothermalzeit-Modells sind aber ungefähre Werte für viele Arten wichtiger als genaue Werte für wenige Arten. Wenn die Mindesttemperatur und die Streuung der Mindestfeuchte aus Veröffentlichungen und Expertenwissen geschätzt würde, können die Hydrothermalzeit und Mindestbodenfeuchte aus vorhandenen Daten von Keimungsversuchen mit nur einer Temperatur- und Feuchtigkeitsstufe berechnet werden. Wir haben unseren Ansatz auf einen Keimungsversuch zum Vergleich der Keimungsquote wilder einjähriger Arten entlang eines Trockenheitsgradienten in Israel angewendet. Mit diesem Ansatz bestimmten wir die Hydrothermalzeit und Mindestfeuchtigkeit von 36 Arten. Der Vergleich mit genauen Werten für drei Arten zeigt, dass mit unserem Ansatz Hydrothermalzeit-Parameter einfach und effektiv bestimmt werden können. Hydrothermalzeit und Mindestfeuchtigkeit sollten auch bestimmte klimabedingte Keimungsstrategien anzeigen. Deshalb testeten wir, ob diese zwei Parameter mit dem Klima am Ursprungsort der Samen zusammenhängen. Wir fanden jedoch keinen für alle Arten übereinstimmenden Zusammenhang, so dass die Unterschiede vermutlich stärker durch standörtliche als durch klimatische Ursachen hervorgerufen werden. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 022 KW - Keimungsrate KW - Dormanz KW - Hydrothermalzeit-Modell KW - einjährige Pflanzen KW - Mittelmeerraum KW - germination rate KW - dormancy KW - hydrothermal time model KW - annual plant species KW - Mediterranean Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-12406 ER - TY - GEN A1 - Köchy, Martin T1 - Photodegradation of grass litter in semi-arid grasslands : a global perspective N2 - In a recent contribution in Nature (vol. 442, pp. 555-558) Austin & Vivanco showed that sunlight is the dominant factor for decomposition of grass litter in a semi-arid grassland in Argentine. The quantification of this effect was portrayed as a novel finding. I put this result in the context of three other publications from as early as 1980 that quantified photodegradation. My synopsis shows that photodegradation is an important process in semi-arid grasslands in South America, North America and eastern Europe. KW - Laubstreu KW - semi-arides Grasland KW - abiotische Zersetzung KW - UV-Licht KW - Schatten KW - leaf litter KW - semi-arid grassland KW - abiotic decomposition KW - UV radiation KW - shade Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-12006 ER - TY - JOUR A1 - Küken, Anika A1 - Gennermann, Kristin A1 - Nikoloski, Zoran T1 - Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana JF - The plant journal N2 - 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. KW - Arabidopsis thaliana KW - constraint-based modeling KW - enzyme catalytic rates KW - kinetic parameter KW - metabolic network KW - turnover number Y1 - 2020 U6 - https://doi.org/10.1111/tpj.14890 SN - 0960-7412 SN - 1365-313X VL - 103 IS - 6 SP - 2168 EP - 2177 PB - Wiley CY - Oxford ER - TY - JOUR A1 - Oberkofler, Vicky A1 - Bäurle, Isabel T1 - Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - A temperature-inducible epigenome editing system to knock down histone methylation can be used to study the role of histone H3K4 methylation during heat stress memory in Arabidopsis.
Histone modifications play a crucial role in the integration of environmental signals to mediate gene expression outcomes. However, genetic and pharmacological interference often causes pleiotropic effects, creating the urgent need for methods that allow locus-specific manipulation of histone modifications, preferably in an inducible manner. Here, we report an inducible system for epigenome editing in Arabidopsis (Arabidopsis thaliana) using a heat-inducible dCas9 to target a JUMONJI (JMJ) histone H3 lysine 4 (H3K4) demethylase domain to a locus of interest. As a model locus, we target the ASCORBATE PEROXIDASE2 (APX2) gene that shows transcriptional memory after heat stress (HS), correlating with H3K4 hyper-methylation. We show that dCas9-JMJ is targeted in a HS-dependent manner to APX2 and that the HS-induced overaccumulation of H3K4 trimethylation (H3K4me3) decreases when dCas9-JMJ binds to the locus. This results in reduced HS-mediated transcriptional memory at the APX2 locus. Targeting an enzymatically inactive JMJ protein in an analogous manner affected transcriptional memory less than the active JMJ protein; however, we still observed a decrease in H3K4 methylation levels. Thus, the inducible targeting of dCas9-JMJ to APX2 was effective in reducing H3K4 methylation levels. As the effect was not fully dependent on enzyme activity of the eraser domain, the dCas9-JMJ fusion protein may act in part independently of its demethylase activity. This underlines the need for caution in the design and interpretation of epigenome editing studies. We expect our versatile inducible epigenome editing system to be especially useful for studying temporal dynamics of chromatin modifications. Y1 - 2022 U6 - https://doi.org/10.1093/plphys/kiac113 SN - 0032-0889 SN - 1532-2548 VL - 189 IS - 2 SP - 703 EP - 714 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Oberkofler, Vicky A1 - Pratx, Loris A1 - Bäurle, Isabel T1 - Epigenetic regulation of abiotic stress memory BT - maintaining the good things while they last JF - Current opinion in plant biology N2 - As sessile organisms, plants have evolved sophisticated ways to constantly gauge and adapt to changing environmental conditions including extremes that may be harmful to their growth and development and are thus perceived as stress. In nature, stressful events are often chronic or recurring and thus an initial stress may prime a plant to respond more efficiently to a subsequent stress event. An epigenetic basis of such stress memory was long postulated and in recent years it has been shown that this is indeed the case. High temperature stress has proven an excellent system to unpick the molecular basis of somatic stress memory, which includes histone modifications and nucleosome occupancy. This review discusses recent findings and pinpoints open questions in the field. Y1 - 2021 U6 - https://doi.org/10.1016/j.pbi.2021.102007 SN - 1369-5266 SN - 1879-0356 VL - 61 PB - Elsevier CY - London ER - TY - GEN A1 - Mao, Hailiang A1 - Nakamura, Moritaka A1 - Viotti, Corrado A1 - Grebe, Markus T1 - A framework for lateral membrane trafficking and polar tethering of the PEN3 ATP-Binding cassette transporter T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 909 KW - precursor indole-3-butyric acid KW - GNOM ARF-GEF KW - plasma-membrane KW - exocyst complex KW - auxin transport KW - planar polarity KW - Arabidopsis-thaliana KW - fluorescent protein KW - soil interface KW - cell polarity Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441302 SN - 1866-8372 IS - 909 SP - 2245 EP - 2260 ER - TY - GEN A1 - Rajasundaram, Dhivyaa A1 - Selbig, Joachim T1 - More effort — more results BT - recent advances in integrative ‘omics’ data analysis T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The development of 'omics' technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of 'omics' data integration together with an overview of available statistical methods and tools. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 923 KW - principal component KW - plant biology KW - package Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-442639 SN - 1866-8372 IS - 923 SP - 57 EP - 61 ER -