Archiv der bisher stattgefundenen Seminare

Raum: Seminar Room

A Pair of microRNAs Controls the Unique Pigmentation Shift in Developing Eggplant Fruit Skin

April 2024

ROS-mediated receptor kinase signalling in plants

March 2024

How do individual subunits of conserved molecular complexes acquire novel functions?

March 2024

Protein homeostasis networks - challenges and opportunities for stressed plants

February 2024

Connection matters: Pi Sensing and ER Quality Control

November 2023

Phosphate status metabolically cues root apical stem cell maintenance via the RGF1-PLT2 regulatory network

November 2023

Nodules and clocks: communication underground

November 2023

Uridylation: a multitasking modification in RNA degradation

October 2023

Feedback control of mitosis in the context of the kinetochore

September 2023

A survey on structural dynamics of energy-converting thylakoid membranes in vascular plants

July 2023

Metabolic arms race between a plant and a fungal pathogen

July 2023

Remodeling the plant cell wall from the inside out

May 2023

Epigenetic control of life cycle transitions in plants and beyond

May 2023

Exploring the genetic diversity of Brazilian Cleomaceae species to understand the evolution of photosynthesis

April 2023

Dissecting the impact of genetic interactions on crop productivity

March 2023

Mastering the maze – how plant sperm reach their mating partners

March 2023

Publishing in Current Biology and Cell Press

März 2023

How do plants optimize photosynthetic light-harvesting under various light conditions?

March 2023

Distributed information processing in plant organs

Februar 2023

LncRNAs, quantitative regulators of level and dynamic of gene expression

Functional genetics of barley stamen maturation

Functional genetics of barley stamen maturation

Exploring the cellular basis of organ curvature using 3D digital ovules

CANCELED --- Christopher J. Marx - A purely Lamarckian "evolution" permits survival of a bacterium to a lethal stressor

Oscar A Ruiz - Lotus spp. as a good tool for productive and environmental objectives in Argentinian agriculture

Antony Dodd - Circadian regulation of plant cell signalling

January 2020

Raphael Trösch - The regulation of chloroplast protein homeostasis: from chloroplast protein import to protein synthesis

Michael Wrzaczek - Cysteine-rich receptor-like kinase 2 coordinates abiotic and biotic stress responses

December 2019

Talia Karasov - Mechanisms of microbial interactions with Arabidopsis thaliana

Nadine Töpfer - Environment-Coupled Models of Leaf Metabolism Capture Mechanisms of Crassulacean Acid Metabolism

November 2019

Anja Schneider - Manganese Transporter in Chloroplasts

Christopher Surridge - Publishing Without Tears

Aalt-Jan van Dijk - Who goes with whom, and why - computational approaches towards understanding of biomolecular interactions

Anne Krapp - Early nitrate signalling by NLP transcription factors in Arabidopsis

Markus Ralser - From its origins to the modern metabolic network

September 2019

Patricia León - Understanding the regulation and possible manipulation of the limiting enzymes of the MEP pathway required for the synthesis of central molecules in plants

September 2019

Jennifer C Ewald - Cross-talk between metabolism and the cell division cycle

August 2019

Iain Johnston

Alex Costa - In vivo calcium dynamics in plant cells: a holistic view

March 2019

Arp Schnittger - The cell biology of genetics

Recombination between homologous chromosomes is a fundamental source of genetic variation andthe basis of nearly all genetics. With this, recombination is also key to evolution and breeding. Theexchange of chromosome segments is accomplished in meiosis and involves tight control ofchromosome behavior, i.e. pairing and synapsis of homologous chromosomes, the formation of DNAdouble strand break and subsequent repair through cross-overs followed by an intricate mechanism toequally distribute the chromosomes to daughter cells. Our research goal is to understand howrecombination is controlled and how the distinct molecular events of the recombination process areorchestrated. We have focused on the cell cycle control machinery and have in particular identifiedCYCLIN-DEPENDENT KINASE A;1 (CDKA;1), the Arabidopsis homolog of the animal and yeastkinases Cdk1 and Cdk2, as a major driving force through meiosis. A substrate search revealed thatmany of the central meiotic regulators are potential CDK phospho-targets. To further elaborate on thecontrol processes of meiosis, we have developed a live cell imaging system that allows us to followchromosome behavior in great temporal and spatial resolution. This imaging system also provides uswith a new possibility to quantify the dynamic processes of meiosis. Here, I will present the latest datafrom our team how differential phosphorylation influences recombination and promotes progressionthrough meiosis. [mehr]

Hiroshi Maeda - Exploiting Evolutionary Diversification of Primary Metabolic Enzymes

November 2018

Anna Amtmann - Unravelling cell-type specific regulatory networks in plant roots

October 2018

Rodrigo Gutierrez

Sean Cutler - Tuning plant water use using abscisic acid receptors

May 2018

Caroline Gutjahr - Arbuscular mycorrhiza development and function

Elisabeth Haswell - Stretching the Imagination: Mechanosensitive Channels in Plants

December 2017

Lars Scharff - Regulation and fine-tuning of protein synthesis in chloroplasts

November 2017

Arndt Telschow

Michal Shapira

Simona Nardozza - The effect of long-term regulation of carbohydrate supply on carbohydrate and anthocyanin metabolism in a red Actindia chinensis var. chinensis genotype

Abstract: Kiwifruit is one of the most recent successful fruit crops on the market. Alongside the well-known green-fleshed Actinidia chinensis var. deliciosa ‘Hayward’, other species with different flavour, shape and colour (yellow and red) have been used in breeding programmes to develop new cultivars. Novel coloured kiwifruit are attractive to consumers, but achieving uniform fruit pigmentation, particularly in red-fleshed Actinidia chinensis var. chinensis genotypes, is challenging. Colour inconsistency between fruit can affect consumer perception, lowering returns to growers. To investigate the cause of colour inconsistency we focused on a solid red-fleshed genotype characterised by variable outer pericarp red pigmentation, we hypothesised that the carbohydrate supply could be responsible for the variation of the red flesh colour. Early in fruit development (28 days after anthesis, DAA) we adjusted the leaf-to-fruit ratio of the shoots to two different carbohydrate supplies (standard and low). Carbohydrate import or redistribution outside of the shoot was controlled by applying a girdle at the base of the shoot, and this girdle was maintained open until harvest to guarantee long-term control of carbohydrate supply. From 84 DAA we observed a reduction in fruit size by about 30 percent, dry matter was reduced by more than 20 percent and colour development by more than 80 percent when fruit had low carbohydrate supply. Both anthocyanin and carbohydrate metabolites were affected. The concentration of major non-structural carbohydrates (starch, glucose, sucrose, and fructose) were also reduced by more than 50 percent in fruit with low carbohydrate supply from 84 DAA. A minor sugar, galactose, was also dramatically reduced by low carbohydrate supply. By 112 DAA, total anthocyanin concentration in the outer pericarp of fruit with low carbohydrate supply was reduced by more than 80 percent. Despite these significant changes in fruit development and metabolites, transcription for candidate genes considered critical steps in the anthocyanin biosynthetic pathway (i.e. GT1, MYB10 and bHLH5) were unchanged between fruit with the two carbohydrate supplies. Interestingly, in low carbohydrate supply fruit, a vacuolar invertase gene (INV3) was upregulated at 112 DAA and a beta-amylase gene (BAM9) was upregulated at 84 and 112 DAA. The upregulation of these two genes could be correlated to the low carbohydrate supply available to the fruit and the need to deplete the starch stored in the fruit to support further development. This work suggested a link between carbohydrate and anthocyanin metabolism, and we now have two further hypothesis to test: i) Galactose is the glycosyl moiety of the main kiwifruit anthocyanin measured in these fruit, and given that galactose content was affected by low carbohydrate supply, repression of colour development could be due to substrate limitation; and/or ii) Carbohydrate depletion could have an effect on an unknown repressor of the anthocyanin pathway. We are currently performing a transcriptomic (RNAseq) experiment to test these hypotheses and results should be available soon. [mehr]

Bernard Carrol - Systemic RNA silencing in plants

July 2017

Cornelia Spetea Wiklund - Thylakoid K+ and Cl- Channels and Transporters Regulate Photosynthesis in a Rapidly Changing Environment

June 2017
Abstract In variable light environments, plants rapidly adjust photosynthesis for an optimal balance between photochemistry and photoprotection. There is increasing evidence that ion fluxes across thylakoid membranes play an important role in regulation of photosynthesis. Recent work from our laboratory have unraveled the roles of the K+/H+ antiporter KEA3, the putative Cl channel CLCe and the voltage-dependent Clchannel VCCN1 in thylakoid ion homeostasis and photosynthetic regulation in Arabidopsis thaliana. However, the current knowledge about these transport proteins comes from the characterization of single loss-of-function mutants of the corresponding genes in Arabidopsis, which do not provide information about possible functional relationships between K+ and Cl fluxes in the thylakoid membrane. In my seminar, I will provide an overview of the current knowledge about genes involved in ion fluxes and regulation of photosynthesis and present data from characterization of higher-order mutants of KEA3, CLCe and VCCN1. Our findings contribute to understanding the thylakoid network of ion fluxes and how they help plants to adjust photosynthesis in variable light environments. [mehr]

Michel Havaux - Singlet oxygen signaling mediated by the apocarotenoid b-cyclocitral in Arabidopsis

Abstract Reactive oxygen species (ROS) are inevitable by-products of photosynthesis. In particular, singlet oxygen (1O2) is intimately associated with photosynthesis since it is produced from the chlorophyll molecules acting as photosensitizers. The ROS produced in the chloroplasts have a signaling function leading to changes in the expression of nuclear genes to adjust the cellular metabolism to the levels of absorbed light energy. The changes in gene expression associated with 1O2 signaling can lead either to cell death or to acclimation to photooxidative stress, depending on the 1O2 production levels. Because of its high reactivity and short lifetime, 1O2 uses mediators for its signaling. Produced in the chloroplast, the b-carotene derivative b-cyclocitral has been identified as an upstream signal molecule in the 1O2 signaling pathway. This talk will summarize our results on the function and mode of action of this apocarotenoid in the acclimation of plants to environmental stresses. [mehr]

Paulo Ferreira - A ROLE FOR THE SUBUNIT 7 OF THE ANAPHASE PROMOTING COMPLEX (APC7) IN THE PLANT IMMUNE SYSTEM RESPONSES

In contrast to animals, plant development is mostly postembryonic; during embryogenesis the main developmental event is the establishment of the root–shoot axis. Organ initiation and growth take place after germination, driven by cell division and differentiation at the meristems. Progression through the cell division cycle requires the temporal and spatial control by regulatory proteins in order to correctly duplicate the DNA and to deliver the newly duplicated genomes to the two daughter cells during mitosis. Cell cycle regulatory components most likely have a bifunctional role in plants. In addition to regulation of the cell cycle process itself, they are involved in the coordination of cell division in the context of a developing organism. Furthermore, at almost every cell cycle, dividing cells at the meristems must integrate development and environmental cues in order to decide whether to go on in another division cycle or to start a new developmental program. CDK/Cyclin activity regulates the transition through cell cycle checkpoints and thereby plant growth and development, and is itself under control of a variety of upstream modules. One of these is the Anaphase Promoting Complex (APC/C), which is an E3 ubiquitin ligase that controls CDK activity by mitosis-promoting cyclins. Besides the well recognized role of the APC during the mitotic cycle, there is increasing evidence that the APC plays a critical role during cell differentiation and development.Here, we show that ectopic expression of the C-terminus portion of the Arabidopsis APC7 subunit accelerates overall plant growth and results in plants with increased biomass production. In addition, the resulting plants are also tolerant to the CaLCuV geminivirus. These results indicate that the APC play active roles in regulation of plant growth and raise the intriguing possibility that the APC may mediate plant immune responses. [mehr]
Plant mitochondria differ significantly from those found in other organisms which has led to the evolution of distinct strategies for genome maintenance, genetic coding, gene regulation, organelle segregation and also protein import pathways. The mitochondrial import apparatus is composed of a number of evolutionary related multi-subunit protein complexes that recognize, translocate and assemble mitochondrial proteins. Our recent work has shown that the translocation pathways found in plant mitochondria are notably different compared to those of other model organisms. We have recently discovered that plant mitochondria contain an essential Twin arginine translocation pathway within the inner membrane. This mitochondrial Tat pathway is at least responsible for the translocation of the Rieske Fe/S protein from complex III but may also have other substrates. Plant mitochondria also contain four members of the YidC/Oxa1/Alb3 family of proteins in contrast to other organisms which normally only contain two. It has been demonstrated that three of these plant Oxa proteins namely Oxa1A, Oxa2A and Oxa2B are essential. The Oxa2A and Oxa2B proteins are unique to the plant kingdom in that they harbor TPR repeats at their C-termini. Our recent work has demonstrated that while the proteins are essential the TPR domain is not. Plants complemented with Oxa2 proteins lacking the TPR domain are viable but severely developmentally delayed. Our recent results in studying the roles and functions of Oxa proteins and the mitochondrial Tat pathway in plant mitochondrial biogenesis will be discussed. [mehr]

Pablo Iván Nikel - Harnessing the metabolic potential of environmental bacteria using SynBio tools

The last few years have witnessed an exponential increase in the number of bacteria that can be used as microbial cell platforms in practical applications. The microorganisms which are the easiest to manipulate genetically (i.e., the so-called "model" bacteria, such as Escherichia coli or Bacillus subtilis) are often not adequate to perform given biotechnological applications (e.g., harsh oxidations or dehalogenation reactions). Contemporary Synthetic Biology endeavors rely on the adoption of specific bacterial chasses for plugging-in and -out genetic circuits and engineer new-to-Nature functionalities. Against this background, environmental bacteria, such as Pseudomonas strains, constitute ideal starting points to design flawless microbial cell platforms, since these microorganisms are pre-endowed with a number of metabolic and stress-endurance traits that are optimal for biotechnological needs. Recent developments on the taming of P. putida for biotechnological applications will be discussed in the context of Synthetic Biology strategies for [i] re-designing the metabolic architecture of central carbon catabolism and [ii] manipulating catalytic biofilms through Synthetic Morphology approaches. [mehr]

A. Harvey Millar - Protein degradation and synthesis rates in leaf growth and development to understand energy use and the maintenance of enzyme function

Proteome studies focus almost exclusively on measuring abundance of proteins and documenting the fact that abundance changes in specific circumstances. This requires detection of statistically significant changes in the protein pool sizes to show that ‘something has occurred’. Protein abundance data are then sandwiched in systems biology models as a layer between transcript responses and metabolite levels. Analysing protein synthesis and degradation rates with progressive stable isotope labelling provides a new window into the control of protein abundance and the energy expended in maintaining the steady-state proteome across genotypes, development and environments1. It provides the first and second derivative of protein abundance with respect to time: how fast are proteins turning over to achieve steady-state or gaining or lowering abundances and do these speeds differ in response to development or the environment? This approach can also enable the relative age distribution of a protein population to be assessed. This has implications for the energetic effort employed by the cell to build or maintain a particular activity and gives clues to the impact of age on the function in different protein types. We are using progressive 15N labelling of Arabidopsis to provide a birds-eye view of the activity of the proteolysis network as it maintains and sculpts the plant proteome. Using peptide mass spectrometry, the progressive labelling of new peptides and the decrease in the abundance of peptides with natural isotope profiles enabled the degradation rate of 1228 leaf proteins to be determined by combining over 60,000 peptide relative isotope abundance (RIA) measurements2. The exponential constant of the decay rate (KD) for each protein during growth showed a wide distribution, ranging from 0 to 2 per day, which was equivalent to protein half-lives of several hours to several months. We are also using this approach to dissect the in vivo action of proteases through analysis of knockout mutants3.We have found new rapidly degrading subunits in a variety of protein complexes, identified the set of plant proteins whose degradation rate correlated positively or negatively with leaf growth rate, calculated the protein turnover energy costs for different leaves and their key determinants within the proteome, and are beginning to interpret transcriptome analyses from the point-of-view of maintenance of the proteome. [mehr]

Karen B. Barnard-Kubow - Patterns of organelle inheritance and genome evolution: characterizing the evolutionary dynamics of a cytonuclear incompatibility

Negative interactions between the organelle and nuclear genomes (cytonuclear incompatibility) are thought to be among the early genetic incompatibilities to arise during speciation. While there are now several good examples of cytonuclear incompatibility leading to reproductive isolation within and between closely related species, there are still many unanswered questions regarding the evolutionary dynamics of cytonuclear incompatibility. Using the herbaceous species Campanulastrum americanum, I examine how patterns of organelle inheritance and rates of organelle genome evolution may both facilitate and constrain the evolution of cytonuclear incompatibility and its ability to drive the early stages of speciation. [mehr]

Ari Pekka Mähönen - Cell Fate Decisions in the Arabidopsis Root Cambium

Despite the importance of the vascular cambium in plant biology and in wood production, the molecular and cellular mechanisms underlying cambial activity remain largely unknown. Particularly, it is unknown where the cambial stem cells are located, and how the stem cell niche is organized to drive cambial growth.In animal stem cell studies lineage tracing has been the method for locating the stem cells. In this method single cell clones marked with reporter expression are generated within a population of dividing cells. The clones are transmitted to all daughter cells of the initial cell, resulting in a marked sector within the tissue. By analysing the size and distribution of the sectors the position and the mitotic activity of dividing cells and stem cells can be deduced. In order to understand the cell lineage relations in the Arabidopsis root cambium, we generated GUS/GFP sectors by using two step CRE-lox based clonal activation system. To understand which cells in the primary tissue contribute to the cambium formation we induced single cell clones during the primary development of the root and analysed the growing sectors during the secondary development. We also generated marked sectors in active cambium to map the position of stem cells and to understand the growth dynamics of the cambial cells. In my seminar presentation I will explain how we are utilizing the lineage tracing data to provide mechanistic understanding of cambium regulation. [mehr]

Keiko Sugimoto - Epigenetic control of plant cell reprogramming

March 2017
Many plant species display remarkable developmental plasticity and regenerate new organs after injury. Local signals produced by wounding are thought to trigger organ regeneration but molecular mechanisms underlying this control remain largely unknown1,2. We have previously identified a group of AP2/ERF transcription factors named WOUND INDUCED DEDIFFERENTIATION1-4 (WIND1-4) as central regulators of wound-induced cellular reprogramming in plants3. More recently we demonstrated that WIND1 promotes shoot regeneration by directly up-regulating ENHANCER OF SHOOT REGENERATION1 (ESR1) encoding another AP2/ERF transcription factor in Arabidopsis4. We have also shown that some of WIND genes and other developmental regulators need to be epigenetically repressed by POLYCOMB REPRESSIVE COMPLEX 2 to prevent unscheduled cellular reprogramming in intact plants5,6. In this talk I will discuss our latest findings on how WIND proteins promote cellular reprogramming and how wound stress activates the WIND-mediated pathway by overriding epigenetic repression. [mehr]

Shizue Matsubara - Long-term acclimation of Arabidopsis to highly fluctuating light environment

Natural light environment is highly variable in both intensity and spectral quality. The light intensity can vary between zero (night) and >2000 μmol photons m-2 s-1 (full sunlight) as the earth rotates, weather changes and wind moves branches and leaves. Upon sudden and large increase in light intensity, photosynthesis is limited biochemically, e.g. by the activation state of RubisCO and the availability of the Calvin-Benson cycle intermediates or inorganic phosphate for ATP synthesis. Low stomatal conductance may also limit plant’s capacity to utilize additional light energy for photosynthesis. When put under highly fluctuating light conditions for days, Arabidopsis plants primarily or initially downregulate photosynthetic light harvesting and linear electron transport while upregulating photoprotection at the expense of carbon gain and growth. Towards understanding the mechanisms of long-term acclimation to highly fluctuating light environment, we studied leaf transcriptome, metabolome and proteome of Arabidopsis (Columbia wild type). Plants were exposed to highly fluctuating light or constant light condition for 3 or 7 days to focus on long-lasting (non-transient) acclimatory changes and downstream responses that may give rise to the phenotypic alterations. Given the pronounced diurnal and circadian variations in leaf metabolism and gene expression, samples were taken at two contrasting time points during the light period in the 12 h/12 h light/dark cycle, namely, early morning and at the end of the day. Furthermore, young and mature leaves were analyzed separately as they typically differ in the photosynthetic capacity. Overall, our results underscore photo-oxidative stress responses and mitigation of acceptor-side limitation to photosynthesis during acclimation to highly fluctuating light. The gene expression profiles revealed distinct responses of young and mature leaves in the morning and at the end of the day, indicating crosstalk between long-term acclimation, leaf development and circadian clock. In particular, I will highlight the changes related to the components of photosynthesis and photoprotection. [mehr]

Ben Field - An unusual nucleotide is a potent controller of chloroplast function that regulates plant growth and development

The chloroplast originated from the endosymbiosis of an ancient photosynthetic bacterium by a eukaryotic cell. Remarkably, the chloroplast has retained elements of a bacterial stress response pathway that is mediated by the signaling nucleotides guanosine penta- and tetraphosphate (ppGpp). However, an understanding of the mechanism and outcomes of ppGpp signaling in the photosynthetic eukaryotes has remained surprisingly elusive. I will present our findings in the model plant Arabidopsis thaliana where we recently showed that ppGpp is a potent regulator of chloroplast gene expression in vivo that directly reduces the quantity of chloroplast transcripts and chloroplast-encoded proteins. We were also able to demonstrate that the antagonistic functions of different plant RelA SpoT homologs (RSHs) together modulates ppGpp levels to regulate chloroplast function, and RSHs are required for optimal plant growth, chloroplast volume, and chloroplast breakdown during dark-induced and developmental senescence. Together our results strongly suggest that ppGpp signaling is not only linked to stress responses in plants but is also an important mediator of cooperation between the chloroplast and the nucleocytoplasmic compartment during plant growth and development. [mehr]

Antonio Granell - Untangling the fruit volatile network

Despite the important contribution of volatile compounds to fruit flavor we still know very little about the molecular genetic basis for volatile production in most fruits. Research using a combination of omics and well characterized genetic resources is changing this situation. I will present some examples of our work on different fruit species that reveals important genome regions and genes for volatile production that can be used for breeding and biotech approaches. [mehr]

Matsuo Uemura - Role of light signals in freezing tolerance mechanism in plants: interactions with temperature signals

Temperate herbaceous plants sense environmental changes during fall and increase their freezing tolerance, which is critical for survival over winter. This process, called as cold acclimation (CA), has been known to be mainly regulated by changes in temperature in season. However, changes in air temperature has been unpredictable and often show sudden risings and/or drops, which is worsened with global climate changes. Light conditions, in addition to lowering temperature, are known as another important factor to regulate CA and, in fact, shortening the day length as well as changes in red/far red light conditions affects the extent of CA. However, effects of light quality and the combination of temperature and light remain to be studied in detail. With Arabidopsis, we here report that light conditions (blue light as well as red light) and temperature conditions in day and night periods (constant vs fluctuated) influence freezing tolerance in complex way. We will discuss elaborate systems for plants to prepare for winter beforehand even under unpredictable climate conditions in the global climate change era. [mehr]

Salim Al Babili - Carotenoids Conversion: It matters where you cut

Carotenoids are characterized by a conjugated double bond system responsible for their vital role in photosynthesis and their colors. This system is also the basis for the function of carotenoids as a platform for the formation of various important compounds, such as retinal, abscisic acid and other signaling molecules. A further example is represented by strigolactones, a novel class of plant hormones that also mediate rhizospheric interactions with root parasitic weeds and mycorrhizal fungi. Carotenoid-derived compounds (apocarotenoids) arise by oxidative cleavage of double bonds, which is catalyzed by Carotenoid Cleavage Dioxygenases (CCDs). CCDs produce compounds with different physicochemical characteristics and biological functions, depending on the site of cleavage. The strigolactone biosynthesis enzyme CCD8 is unusual CCD since it catalyzes the cleavage of a single bond, in combination with other different reactions. In this talk, we will give an overview about apocarotenoid formation, focusing on the biosynthesis of striglactones. We will also show how basic knowledge about this pathway can be applied to combat root parasitic weeds. [mehr]

Siobhan M. Brady - Transcriptional regulation of plant metabolism

Regulation of plant development requires intricate communication with both primary and specialized metabolism in order to fuel growth. While transcriptional regulation of metabolism is evident from myriad whole genome-expression analyses, our understanding of which transcriptional regulators are responsible for these changes as well as their underlying mode of action is unclear. I will highlight our efforts on systematic mapping of transcriptional regulators of nitrogen metabolism, the tricarboxylic acid cycle and glucosinolate biosynthesis. Network analyses incorporating protein-DNA interaction data, gene expression and connectivity were used to identify critical regulators, most of which were shown to regulate growth and metabolism in planta. Finally, these analyses have shed light on modularity within these pathways and global perspectives on this additional mode of plant metabolic regulation. [mehr]

Sam Seeman - Protein Targeting to STarch: A new class of proteins that bring enzymes and substrates together

Starch is a vital plant product, being the major nutritive component of our staple crops and an important feedstock for industry. Starch takes the form of insoluble, semi-crystalline granules composed of two glucose polymers: branched amylopectin and near-linear amylose. Amylopectin, the major component, is responsible for the semi-crystalline nature of starch. It is made by a set of enzymes; starch synthases, branching enzymes and debranching enzymes. In contrast, amylose is made within the amylopectin matrix by a single enzyme – Granule-Bound Starch Synthase (GBSS) – that becomes trapped as amylopectin crystalizes about it. There is much that we still do not understand about starch biosynthesis, such as how the enzyme activities are coordinated and how starch granules are first initiated. We recently discovered that a new class of proteins is required to localize some of the Starch Synthase activities. We called these proteins PTST (for Protein Targeting to Starch). Arabidopsis has three PTSTs. PTST1 binds GBSS and delivers it to the starch granule surface, whereupon it dissociates and leaves GBSS to synthesise amylose. In the absence of PTST1, GBSS fails to localize to the granule and the starch is composed solely of amylopectin. In contrast, PTST2 and PTST3 bind to another starch synthase, SS4, which is implicated in starch granule initiation. Defects in SS4 or in PTST2/3 significantly alter the number, size and shape of starch granules without necessarily affecting the structure or ratio of the constituent polymers. We believe that these PTSTs bind low-abundance precursors from a pool of malto-oligosaccharides and deliver them to SS4 for elaboration into starch granule initials. In this talk I will summarize these and other results which shed new light onto how plants make starch. [mehr]

Marja Timmermans - Small RNAs as mobile, morphogen-like signals in development

Abstract: Small RNAs as mobile, morphogen-like signals in development Damianos Skopelitis1, Anna Benkovics1, Aman Husbands1 and Marja Timmermans1,2 1) Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA 2) Center for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, 72076 Tuebingen, Germany Adaxial-abaxial (top-bottom) polarity drives the flattened outgrowth and patterning of leaves, and represents an important innovation in the evolution of land plants. Patterning of this axis is driven by an intricate gene regulatory network. Integral to this network are two sets of conserved transcription factors that promote either adaxial or abaxial fate, and are expressed in complementary domains on the top or bottom side of the leaf, respectively. The positional information needed to delineate these domains is provided in part by the small RNAs miR166 and tasiR-ARF. We have shown that these small RNAs move outside their defined domain of biogenesis and form opposing gradients across the leaf that polarize expression of key adaxial- and abaxial-promoting transcription factors, HD-ZIPIII and ARF3/4, respectively. Our observations, which will be presented, indicate that mobile small RNAs have the inherent capacity to generate sharp gene expression boundaries, and function as morphogen-like signals in development. Their patterning properties present small RNAs and their targets as highly portable regulatory modules through which to create pattern, and provides a compelling basis for the extensive conservation and repeated co-option of developmentally important small RNA-target modules. [mehr]

Steve Penfield - Control of progeny seed behaviour by the mother plant

Abstract: During reproduction the mother plant uses environmental signals to modulate the dormancy and behaviour of her progeny seeds. This presentation will explore the importance of this process in plant evolutionary biology, and discuss what is known about the underlying molecular mechanisms. Key data will point to an ancient role of flowering time genes in seed biology, which may precede the co-option of these genes into reproductive processes that evolved later, such as flowering itself. Using natural variation to study seed dormancy I will raise the prospect that a parental conflict exists at the heart of seed dormancy and growth vigour, and therefore that mothers and fathers have different optimised fates for progeny seeds. We can speculate a bit as to why this might be and the implications for crop science. [mehr]

Zach Adam - Deg proteases in the thylakoid lumen - are they 'more of the same'?

January 2017
Prokaryotic Deg (HtrA) proteases are involved in protein quality control and response to stress [1]. The Arabidopsis thaliana genome contains 16 Deg genes whose products are distributed in chloroplasts, mitochondria, peroxisomes and the nucleus [2]. Deg2 and Deg7 are located in the chloroplast stroma, whereas Deg1, Deg5 and Deg8 are found in the thylakoid lumen. Deg1 forms active homo-hexamers at acidic pH, degrading photosynthetic proteins, especially in relation to the PSII repair cycle [3,4]. Deg5 and Deg8 form hetero-complexes, performing apparently similar functions [5], raising the question whether the two complexes are redundant. To answer this, we generated a full set of single, double and triple KO mutants and compared their phenotypes. We found that under optimal growth conditions Deg5-Deg8 mutants look like WT, but Deg1 mutants are smaller and show higher sensitivity to photoinhibition. Under harsher conditions, Deg5-Deg8 mutants are also affected, although less than Deg1 mutants. However, the functions of the two complexes are somewhat redundant, as overexpression of Deg5-Deg8 can partially compensate for the loss of Deg1. Comparative proteomics revealed in the triple mutant moderate up-regulation of thylakoid proteins involved in folding, translocation, assembly and degradation, and down-regulation of components of all photosynthetic complexes. Testing the steady-state level of the thylakoid Deg proteases in WT plants demonstrated that Deg1 is approximately two-fold more abundant than the Deg5-Deg8 complex. Moreover, recombinant Deg1 had higher in vitro proteolytic activity compared with Deg5, Deg8 and the combination of the two. These results suggest that the differences in abundance and proteolytic activity are the source of the differential importance of the two complexes in vivo. [mehr]

Paolo Pesaresi - GUN1, a Jack-Of-All-Trades in Chloroplast Protein Homeostasis and Signaling

Dezember 2016
Abstract: The GENOMESUNCOUPLED1 (GUN1) gene has been reported to encode a chloroplast-localized pentatricopeptide-repeat protein, which acts to integrate multiple indicators of plastid developmental stage and altered plastid function, as part of chloroplast-to-nucleus retrograde communication. However, the molecular mechanisms underlying signal integration by GUN1 have remained elusive, up until the recent identification of a set of GUN1-interacting proteins, by co-immunoprecipitation and mass-spectrometric analyses, as well as protein–protein interaction assays. Here, we review the molecular functions of the different GUN1 partners and propose a major role for GUN1 as coordinator of chloroplast translation, protein import, and protein degradation. This regulatory role is implemented through proteins that, in most cases, are part of multimeric protein complexes and whose precise functions vary depending on their association states. Within this framework, GUN1 may act as a platform to promote specific functions by bringing the interacting enzymes into close proximity with their substrates, or may inhibit processes by sequestering particular pools of specific interactors. Furthermore, the interactions of GUN1 with enzymes of the tetrapyrrole biosynthesis (TPB) pathway support the involvement of tetrapyrroles as signaling molecules in retrograde communication. [mehr]

Jenny Russinova - Trafficking of Plant Receptor Kinases: When the Intracellular Logistics Matters

Abstract: Receptor-mediated endocytosis is an integral part of signal transduction, as besides signal attenuation, by removal of activated receptors and their bound ligands from the cell surface, it allows the spatial and temporal regulation of the signaling outputs from the endosomes. After receptors have been activated and internalized, they can be separated from their ligands and recycled back to the plasma membrane or transported for degradation. Crucial in the study of the interplay between endocytosis, recycling, and signaling of plant receptor kinases is the development of imaging tools (bioactive fluorescent probes) to visualize membrane-associated signaling events at a high spatiotemporal resolution. Recently, we have been able to view endocytosis of different receptor kinases in living Arabidopsis thaliana cells using fluorescent small-molecule and peptide ligands. In addition, we are exploring the chemical biology for development of novel specific endocytosis inhibitors that will contribute to the better understanding of how this process regulates signaling outputs in plants. [mehr]

Magalie Uyttewaal - Regulation of Plant Cell Growth and Division by new Family of Microtubule Associated Proteins

Abstract:The presence of reproducible developmental patterns and shapes in plants underlies mechanisms that ensure the robustness and coordination of cellular processes such as cell division orientation and cell growth. When a plant cell divides, a new wall is built that connects existing ones and separates daughter cytoplasms. This wall firmly binds every plant cell to its neighbors and prevents any migration. As a consequence, the topology of plant tissues mostly results from the orientation of mitoses and cell growth. Every aspects of cell growth and division involve the microtubule cytoskeleton with specialized microtubule arrays that accompany each stage of plant cell development.We have identified a major organizer of cortical microtubule arrays, the TTP complex (which contains TON1, TRM and PP2A proteins), and were able to uncouple its role in interphase from its role in mitosis by isolating specific G2/M and interphasic isoforms. The contributions of these specialized isoforms to the robustness of cell growth, cell division and plant development will be presented. [mehr]

Łucja Kowalewska - 3D Visualization of Thylakoid Membrane Development

Abstract: Chloroplast biogenesis is a complex process that is integrated with plant development, leading to fully differentiated and functionally mature plastids. At the structural level of chloroplast biogenesis, the regular network of paracrystalline prolamellar bodies (PLBs) and the flattened porous membranes of prothylakoids develop into the chloroplast thylakoids. Three-dimensional reconstruction is required to provide us with a more complete understanding of this transformation. We used electron tomography and confocal microscopy to reconstruct the process of structural membrane transformation during the etioplast-to-chloroplast transition in runner bean (Phaseolus coccineus). We also point out the importance of particular chlorophyll-protein complex components in the membrane appression during the subsequent stages of biogenesis process. We provide 3D models of the bean chloroplast biogenesis that allow spatial reconstruction of the internal membranes of the developing chloroplast and visualize the transformation from the tubular arrangement to the linear system of parallel lamellae. The results show that the transformation of PLBs consists of the untwining of tubules from the PLB structure in a continuous process, without dispersion to vesicles. The tubular structure of the PLB transforms directly into flat slats that eventually form grana. We demonstrate that grana membranes, from the beginning of their formation, associate with stroma thylakoids in a helical way. The main structural stages of chloroplast internal membrane biogenesis are presented in a movie that shows the time development of the chloroplast biogenesis as a theoretical dynamic model of this process. [mehr]

Michael Knoblauch - New Insights on the Physiology and Cell Biology of Phloem Transport and Unloading

Abstract: Vascular systems allow organisms to distribute resources internally by bulk flow and thus to overcome size limitations set by diffusion. In plants, the evolution of vascular tissues enabled the development of trees and forests and was accompanied by a major increase in the productivity of terrestrial ecosystems. The process of phloem transport and unloading plays a critical role in allocating photoassimilates to sinks which in form of cereals, tubers, roots etc. represent the major food sources for humans. The cellular processes of phloem transport and allocation control at the site of phloem unloading, however, are hardly investigated and poorly understood. Recent data suggest that the current model of phloem unloading - the high pressure manifold model - does not accurately describe the events in the unloading zone. New data on the physiology and cell biology of phloem transport and unloading will be pressented. [mehr]

Gary Stacey - Application of soybean genomic tools to the study of the nitrogen fixing, rhizobium symbiosis

The successful completion of the soybean genome sequence in 2010 enabled the application of the full range of genomic tools and methods to the study of the nitrogen fixing rhizobial symbiosis. This symbiosis is the result of infection of soybean roots by the soil bacterium, Bradyrhizobium japonicum. In order to more precisely study the early infection events during the establishment of this symbiosis, my laboratory pioneered the use of isolated root hair cells as a single cell model for systems biology. We have applied the full repertoire of functional genomic methods to this system characterizing, for example, the transcriptome, proteome, phosphoproteome, miRNA, DNA methylation, and others. These studies, within the context of a general focus on soybean genomics, has enabled us to compile a large dataset, which has provided novel insight into the mechanisms by which the nitrogen fixing symbiosis is established. Among these important insights is the growing realization that the plant innate immunity system plays an important role in the symbiosis. [mehr]
At the interface of plant science, policy, economy and public - and how to get thereScience management and communication are key elements of successful research programs. PLANT 2030 is a BMBF funded competence network of applied plant science in Germany as well as international collaborations. In the managing office, we interconnect plant scientists and we are the central hub for the communication between science, policy, plant breeding and the public. In our talk, we will give insights into our day-to-day business as well as strategies in the longer term. We will examine different ways of career development in our field giving examples of educational programs as well as trainings on the job. All three of us having different vocational backgrounds, we cover a range of expertise and will give you an overview on diverse job opportunities in the heterogeneous field of science management and communication. [mehr]

Jane Mellor - Gene Regulation: Sense, antisense and non-coding transcription and transcript fate

November 2016
Eukaryotic genomesare pervasively transcribed in gene rich regions leading to the production of avariety of transcripts including coding pre-mRNAs, antisense transcripts, di-cistronic transcripts and other long non-coding transcripts. We havediscovered that many transcripts are unstable, or are retained in thenucleus, raising interesting questions about how the differential fate oftranscripts is determined. Using Saccharomyces cerevisiae as a model system, firstwe show that the Isw1 chromatin remodelling ATPase retains poorly processedtranscripts in the nucleus. Second, we have developed a novel nucleotideresolution, strand-specific technique to map the association oftranscription elongation factors with RNA polymerase II. We show thatlevels of Paf1 on RNA polymerase II contribute to the fate of the encodedtranscripts, with low levels associated with nuclear retention oftranscripts. Finally using mathematical modelling, we show how antisensetranscription influences sense transcription and transcripts. [mehr]
SNARE proteins catalyse the final step inmembrane fusion with their cognate SNARE partners through tight interaction viatheir cytosolic N-terminal domains. Their C-terminal membrane anchor pulls theopposite membranes together, overcoming the strong dehydration forces associatedwith the lipid bilayer and ultimately leading to fusion of the two membranes.This important function is prerequisite to a multitude of vital cellularfunctions such as trafficking of cargo to the outside of the cell or addingadditional membrane material to the plasma membrane for expansion.In yeast and mammals integration oftail-anchored (TA) membrane proteins seems to be facilitated via cytosoliccomponents in an ATP-dependent fashion. This ‘Guided-Entry of TA proteins’(GET) pathway has not been described in plants where research focusses on theimport pathways into chloroplasts and mitochondria. How the abundance of SNAREand other important TA proteins are integrated into the ER membrane in plantsis currently entirely unknown.We have identified the candidates involved in aputative GET pathway of Arabidopsis.Our data show that plants have evolved multiple orthologues of specific GETpathway components, albeit in a compartment-specific manner. In contrast,others seem to be absent in plants suggesting differences in the proteininsertion mechanism or the development of alternative pathways. The latterhypothesis is supported by highly specific rather than general phenotypesassociated with loss-of-function lines highlighting the plant’s need for backupinsertion mechanisms. [mehr]
Chloroplast signals that impactleaf developmentThe most conspicuousfunction of chloroplasts is photosynthesis. However, these organelles alsofunction as factories that synthesized a pletora of essential compounds forplant life. Chloroplasts are thus central an enviromental sensor of the cell,and this information is transmitted to the ncucleus through retrogradesignaling, modulating the expression of nuclear-genes to fine-tune the generalplant developmental and external responses. Recent advances have demonstratedthe existence of multiple retrograde signaling pathways, but only few signalsresponsible for this regulation have been identified.  In recent years,evidence has supported that apocarotenoids are important signals that regulatediverse aspects of plant and animal development. The characterization of an Arabidopsisclb5 mutant, impaired in early chloroplast development, provided geneticand molecular evidences that the accumulation of apocarotenoid profoundlyaffects nuclear and plastid gene expression as well as leaf development. Thealbino clb5 mutant of Arabidopsis displays a unique defect in themorphology of the leaf with radial shape and defects in leaf polarity, that isnot observed in other albino mutants supporting the idea that chloroplaststatus is tightly monitored and strongly correlated with leaf development.These phenotypes are a consequence of the defect in the zeta carotenedesaturase (ZDS) activity that results in the accumulation of phytofluene andz-carotenoid intermediates. Our work also demonstrates that the signal responsiblefor the clb5 phenotypes is produced through specific cleavage ofphytofluene or z-carotenoids by the CCD4 enzyme. Furthermore, theanalysis of gene expression for ZDS and CCD4 shows an correlation acrossmultiple tissues and developmental stages. Using wide genome analysis, we havefound that this signal affects the expression of key nuclear-encoded genesimportant for leaf and plastid development as well as genes from thechloroplast genome in comparison to the carotenoid-deficient pds3 mutantplant, supporting the unique role that these carotenoids have over plantdevelopment. Finally, we found that the regulation on gene expression dependson specific cis-acting sequences located in the promoter region of thetarget genes. [mehr]
Cells usestructure to catalyze and facilitate the chemical reactions of metabolism. Thisprinciple is exemplified by the process of carbon dioxide assimilation inphotosynthetic cyanobacteria, which coordinate myriad biochemical components inspace and time, in order to achieve a single physiological goal – convert solarpower into fixed chemical energy. An essential player in this process is thecarboxysome, a protein-based organelle composed of an icosahedral proteinshell, which encapsulates the enzymes RuBisCO and carbon anhydrase within a~100 nm structure. Despite knowledge of the overall structure of thecarboxysome, much less is known about the molecular interactions driving itsself-assembly and how this process is capable of occurring in the complex invivo environment. Here, I describe our biochemical efforts to elucidate amechanistic picture of how the carboxysome assembles and functions in the cell.At the same time, our lab is also interested in developing a holistic pictureof how a coordinated physiology emerges from the many different proteinactivities, including the carboxysome and numerous transporters, found incyanobacteria. To this end, I present our recent efforts at reconciling theseactivities using a mathematical reaction-diffusion model of carbon dioxideassimilation. Finally, a general challenge to studying physiology is the lowthroughput of assays for quantifying metabolism. I therefore conclude with ourefforts at using protein engineering for constructing fluorescent metabolitebiosensors and enabling high-throughput studies of metabolism. [mehr]
We are exploringhow plants execute and fine-tune their developmental programs in response tointernal and external cues that rely on plant hormone signaling. In particularwe are interested in the transcriptional and post-transcriptional regulationduring early developmental decisions, such as giberellic acid (GA)-regulatedsex determination in 3-6 cell fern gametophytes, or strigolactone (SL)-inducedrepression of branching via arrest of axillary meristems in garden pea. Ourexperimental approaches rely on next generation sequencing to identify andquantify coding and non-coding transcripts in plants without reference genomesequence (but otherwise excellent model organisms). I will illustrate how planthormones can have very different effects on gene expression throughoutdevelopment. In fern gametophytes GA induces extensive transcriptome (andlikely epigenome) reprogramming, where we discovered over 1100 genes affectedby GA, mostly up-regulated, including signatures of extensive chromatinremodeling, activation of several hormone signaling cascades, and extensivechanges in non-coding RNA, including microRNA, well before any morphologicaldifferences can be observed. In contrast, we found that SL induces small butvery fast and specific transcriptional responses in garden pea axillary buds,including several key transcription factors, implicating other hormonesignaling pathways, as well as post-transcriptional and post-translationalcontrol in the regulation of branching. [mehr]

Diana Santelia - Starch metabolism in guard cells

Michele Zaccai - Exploring the regulation of flowering in lily

August 2016
Lilium longiflorum (Easter lily) is a leading ornamental bulbouscrop worldwide. Lily flowering time is primarily controlled by cold exposure(vernalization). We investigated the response of lily to vernalization using atranscriptome assembled from meristems of cooled and non-cooled bulbs, followedby expression analyses and gene annotation. Full cDNA coding sequences ofseveral genes overexpressed in lily and Arabidopsis altered their floweringtime. Other experiments showedthat, contrarily to the common assumption, Easter lily doesn't have anobligatory requirement for vernalization and that bulb size controls floweringpathways. [mehr]

Jan Traas - Flower development: from morphodynamics to morphomechanics

Flower development : from morphodynamics to morphomechanics The shoot apical meristem (SAM) continuously generates leaves, flowers, and branches in higher plants. In the past decades, many components of the gene regulatory networks in the SAM have been identified. However, little is known about the spatiotemporal coordination between gene expression patterns and growth at cellular resolution. This lack of understanding is mainly due to the lack of comprehensive quantification of organ wide cell properties over time with regards to the underlying molecular networks. We address this problem in early flower development of Arabidopsis thaliana using high resolution confocal time lapse imaging, combined with genetic and biophysical approaches. Hereby we are focusing on the cell wall, which plays a central role in the control of growth rates and growth directions. Recent relevant publications from our team : Ali O, Traas J* (2016) Force-Driven Polymerization and Turgor-Induced Wall Expansion. Trends Plant Sci. 2016 May;21(5):398-409. Theoretical analysis. Boudon F, Chopard J, Ali O, Gilles B, Hamant O, Boudaoud A, Traas J*, Godin* C. (2015) A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution.PLoS Comput Biol. 2015 Jan 8;11(1):e1003950. Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. (2014) An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis . Curr Biol. 2014 Oct 6;24(19):2335-42 Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. (2012) The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol Syst Biol. 2011 Jul 5;7:508. [mehr]
Photosynthesis light-use efficiency is fundamentally constrained by the light-limited quantum yield for carbon dioxide fixation, which under non-photorepiratory conditionsis as good as light-use efficiency gets. Normally assumed to be 0.125 - the magic number in photosynthetic quantum yields, it is actually less than this,and shows wavelength dependency. Despite its importance, this limiting quantum yield is not much studied or quantitatively understood. Some years ago we analysed the spectral-dependency of the light-limited yield for carbon dioxide fixation in cucumber, and we have repeated and extended this work for tomato.In addition to simple absolute quantum yield measurements we also, for tomato,examined the impact of state-transitions on carbon fixation yields, something which has not so far (to the best of our knowledge been) done. In addition to carbon dioxide fixation under light-limited conditions we also measured parameters associated with PSII and PSI efficiency. These results will be reported.  We have also developed equipment that allows us under a range of controlled conditions (varying irradiance, carbon dioxide and oxygen concentrations, and temperature) to measure, more or less concurrently, parameters associated with efficiency and regulation of light-use efficiency by PSI and PSII, and carbon dioxide fixation. With this we can build quite a complete picture of how photosynthesis in vivo proceeds and is regulated as a multicomponent system.Some of the results we have obtained do not seem to be consistent with the simple model(s) of regulation that have been developed over the last few years.Data will be presented to illustrate some of the anomalies we feel we have uncovered. [mehr]
Second generation sequencing has caused major breakthroughs in the use of archival DNA, and in the use of herbarium specimens in particular. Whereas this enables testing of historical biological hypotheses, concerns remained about accuracy of herbarium sequence data and the possibility of post-mortem damage. Using a panel of angiosperm trees we compared fresh and historic samples of the same individuals and concluded that such damage is negligible, and that specimen age per se does not predict sequencing success. 2nd generation sequencing retrieves herbarium plastomes surprisingly well, which opens up possibilities for further taxonomic and time sampling. One such clades is Pelargonium (Geraniaceae) which is well-known for its horticultural importance as well as its elevated levels of (organellar) genomic evolution, or genome instability. Whereas some family members have lost Inverted Repeats alltogether, the hybrid P x hortorum is usually cited as having the largest Inverted Repeats known in angiosperms. However, to what extend this is a natural phenomenon or a ‘breeding artefact’ remains to be ascertained. In addition, it is in this Pelargonium clade that both bi-parental inheritance and cytonuclear incongruence occurs. In the context of increased taxonomic sampling of plastomes around the parent species of P x hortorum, be it from herbarium or fresh material, we hope to elucidate this and other questions further. [mehr]

Jerry Eichler - Sweet and Extreme: N-glycosylation in the Archaea

July 2016
It is now clear that N-glycosylation, the covalent linkage of glycans to select asparagine residues of target proteins, is a post-translational modification that occurs across evolution. While understanding of the eukaryal and bacterial versions of this universal protein-processing event is relatively advanced, far less is known of N-glycosylation in Archaea. This, despite the fact that N-glycosylation is seemingly widespread in Archaea and that archaeal N-linked glycans present diversity in composition and structure not seen elsewhere. Relying on the halophilic archaea Haloferax volcanii, originally isolated from the Dead Sea, as a model system, work in our group has tried to fill this void. Accordingly, bioinformatics, genetic, mass spectrometry and biochemical approaches have been employed to delineate the pathways used for the assembly of two distinct glycans N-linked to target proteins in Hfx. volcanii. The same general strategy is now being used to better understand N-glycosylation pathways in other Archaea. As such, our studies on archaeal N-glycosylation not only expand understanding of a universal post-translational modification, they also provide novel insight into life at extremes. [mehr]

Richard S. Smith - Quantifying morphogenesis with MorphoGraphX

Morphogenesis emerges from complex interactions between genetic and mechanical processes. Computer simulation models are becoming increasingly important to aid our understanding of the complexity involved, in an emerging field that is now being called Computational Morphodynamics. Key to this methodology is the combination of experimental work with dynamic, spatial simulation modeling. In order to analyze shape change in developing organs, it is essential to be able to quantify cell shape and gene expression changes at cellular resolution, over multiple time points. Ideally, a full 3D quantification of shape change and gene reporter expression over time is desired. Unfortunately, this is often technically challenging. In cases where the processes of interest occur on a surface layer of cells, 2D (i.e. max) projections can be used. However on highly curved organs and tissues, flat projections can introduce too much distortion to accurately record cell shape change. Here I will present a new image processing software called MorphoGraphX that bridges this gap by working directly with curved surface images extracted from 3D data. After recognizing the shape of a 3D sample, the surface is extracted and the signal is projected on the surface to form a curved “2.5D” image. I will demonstrate many of the tools we have developed to enable image processing on these 2.5D images, and how to use them to quantify 4D confocal time-lapse data sets. Finally, I will present our inroads towards developing an integrated simulation and imaging environment for Computational Morphodynamics. [mehr]
Antibodies are a popular tool used in plant cell biology research. They can be either custom made or purchased from a commercial supplier. In either case their production is a complex process, consisting of three very important components which has to be carefully considered. These are: Antigen-Animal-Testing. Which source of antigen is most optimal for your project: peptide, recombinant protein or a native protein isolated from tissue? Which animal species to choose? Are certain species making better antibodies compare to others? Do I have any controls to validate produced antibody? What controls should be used? What to do if my antibody is not giving any signal in a western blot? [mehr]
Drought and soil salinity represent two tightly linked abiotic stress factors. Together they by far cause the most damaging effects on annual crop yields. Although evidence for the importance of the chloroplast in surviving these adverse environmental effects have existed for years still the molecular processes are not well understood. Recently, several independent laboratories have started to investigate the plastid ion transport mechanisms. Particularly K+ flux was found to be crucial in maintaining the chloroplast ion and pH homeostasis and to fine-tune photosynthesis. This carefully balanced system can be readily disturbed by abiotic stress. For instance, during salt stress toxic Na ions also accumulate in chloroplasts, where they replace K+ ions and diminish photosynthetic efficiency in plants. This could supposedly be prevented by controlling the ion flux across the envelope membrane via ion carries and channels. The kea1kea2 mutant that lacks two highly active K+/H+ antiporters is strongly growth compromised with poor photosynthesis under normal growth conditions. However, if exposed to soil salinity mutants flourish with highly recovered photosynthetic efficiency. My lab is interested in deciphering the molecular foundation of this phenomenon. By doing so, we anticipate to find the missing ion transport mechanisms in the envelope membrane. In my seminar I will show some early data on how we approach this endeavor and what we plan to do in the next few years. [mehr]
Ascorbic acid (vitamin C) is a major antioxidant in plants, and fruits are the major source of this vitamin for humans. While the pathways of synthesis, recycling and degradation are well characterized, their regulation is still poorly understood. We have used reverse genetic approaches to target two key steps of the Wheeler & Smirnoff synthesis pathway: GDP-D-mannose epimerase (GME) and GDP-L-galactose phosphorylase (GGP) in tomato fruits. In addition to a reduction of ascorbic acid content, RNAi-silenced gme tomato lines exhibited growth phenotypes resulting from cell division and expansion defects, exacerbated fragility and loss of fruit firmness related to modifications of the cell wall structure and composition [1,2]. These findings help to explain observed links between seemingly unrelated quality traits such as fruit firmness and ascorbic acid content. Two ggp knockout lines were identified from TILLING (EMS) mutant populations. These have reduced ascorbic content and show bleaching and leaf necrosis after short exposure to high light [3,4]. Integration of transcriptomic, proteomic, and metabolomic data from wild type and mutant tomato fruits identified candidate genes involved in the regulation of the ascorbate pathway [5]. A forward genetic screen has identified four mutant lines which have 2.5 to 5-fold higher levels of ascorbic acid than wild-type, and one candidate gene has been mapped using next generation sequencing approaches. [1] Gilbert L, Alhagdow M, Nunes-Nesi A, Quemener B, Guillon F, Bouchet B, Faurobert M, Gouble B, Page D, Garcia V, Petit J, Stevens R, Causse M, Fernie AR, Lahaye M, Rothan C and Baldet P. (2009). Plant J. 60, 499-508. [2] Voxeur A, Gilbert L, Rihouey C, Driouich A, Rothan C, Baldet P and Lerouge P (2011). Journal of Biological Chemistry, 286: 8014-8020. [3] Okabe Y, Asamizu E., Saito T., Matsukura C., Ariizumi T., Bres C., Rothan C., Mizoguchi T. and Ezura H. (2011). Plant Cell Physiol. 52(11): 1994–2005. [4] Just D., Garcia V., Fernandez L., Bres C., Mauxion JP., Petit J., Jorly J., Assali J., Bournonville C., Ferrand C., Baldet P., Lemaire-Chamley M., Mori K., Okabe Y., Ariizumi T., Asamizu E., Ezura H., and Rothan C. (2013). Plant Biotech. 30, 225-231. [5] Garcia V., Stevens R., Gil L., Gilbert L., Gest N., Petit J., Faurobert M., Maucourt M., Deborde C., Moing A., Poessel JL., Jacob D., Bouchet JP., Giraudel JL., Gouble B., Page D., Alhagdow M., Massot C., Gautier H., Lemaire-Chamley M., de Daruvar A., Rolin D., Usadel B., Lahaye M., Causse M., Baldet P. and Rothan C. (2009). Compte rendu de Biologie. 332, 1007-1021. [mehr]

Uri Pick - How are triacylglycerides produced in the green alga Dunaliella tertiolecta?

June 2016
Green microalgae accumulate under stress conditions such as nitrogen limitation either starch or triacylglycerides (TAG) or both. The biosynthesis of TAG is of special interest because it is a potential source for production of biodiesel. However, there are still large gaps in our understanding about the enzymatic pathways of TAG biosynthesis and how it is controlled. This work was designed to clarify two issues in triacylglyceride (TAG) biosynthesis in green algae: what is the major rate-limiting stage in TAG biosynthesis and how much fatty acids (FA) that are channeled for TAG biosynthesis are produced de novo, from pre-formed polar lipids (PL) or from degradation of starch. The work was performed in the halotolerant alga Dunaliella tertiolecta by pulse labeling with 14C-palmitic acid (PA) and with 14C-bicarbonate. The results show that: (i) FA biosynthesis is the rate-limiting stage in TAG biosynthesis and it precedes the activation of glycerol transacylation into TAG, (ii) degradation of pre-formed lipids provides less than 10% of the FA in TAG, (iii) starch provides over 90% of the carbon for FA biosynthesis and as such is the major carbon source for FA and TAG biosynthesis under N deprivation, (iv) under control (+N) conditions, most FA are initially incorporated into phosphatidylcholine (PC). Under N deprivation incorporation into PC is inhibited, whereas incorporation into digalactosyldiacylglycerol (DGDG) is enhanced, suggesting that DGDG serves as an intermediate in acyl transfer into TAG. The significance of these results for our understanding of TAG biosynthesis and for future advances in improving TAG productivity in algae will be discussed. [mehr]
Current metabolomics techniques provide only a static view on metabolite amounts present inside or outside of living cells. Stable-isotope labeled tracers can be applied to obtain dynamic information on biochemical reaction networks. However, such methods like for example Metabolic Flux Analysis (MFA) only provide information on known compounds in a targeted manner and rely on extensive a priori knowledge. To shed light on yet unknown parts of the metabolism, we developed the Non-targeted Tracer Fate Detection (NTFD) methodology to detect all known and unknown compounds derived from a stable-isotope labeled tracer present in a GC/MS chromatogram. For every detected and labeled compound mass isotopomer distributions (MIDs) are determined. MIDs of known and unknown compounds are then used as input for the Mass Isotopolome Analyzer (MIA). Based on the non-targeted labeling data, this software reveals global flux changes in known and unknown parts of the metabolic network. During my presentation I will introduce these tools and provide examples on how we applied those to address biological problems in our research and highlight unexpected findings: 1. I will report about a new metabolic driven antimicrobial defense mechanism in macrophage and microglial cells. By using non-targeted metabolomics, we identified a metabolic pathway that these immune cells apply to produce high amounts of an antimicrobial metabolite. 2. By the application of MIA to analyze GC/MS data of stable-isotopic labeled cell extracts of lung cancer cells, we found the neuronal compound N-acetyl-aspartate (NAA) and a neuro-peptide in these cells. We could show that NAA aspartate is involved in fatty acid synthesis and that it is important for fast proliferation. [mehr]
Growth and maintenance processes requiring carbon must be maintained despite daily fluctuations in light and dark conditions. Buffering against daily fluctuations in the carbon supply is achieved through a diel turnover of starch. Starch accumulates in the day and decreases in the night with almost linearly. Moreover, starch accumulates rapidly and decreases slowly as night-period decreases, which allows plants to maintain the same amount of starch at the end of the night regardless of photoperiod. Recent studies reported the importance of feedbacks between circadian clocks and carbon metabolism for optimal growth. However how plants adjust starch metabolism in response to changing photoperiod remains elusive. To investigate the mechanism of flexible coordination of starch metabolism, we modeled the interplay of carbon metabolism and circadian clocks. We first showed that the linearity of starch metabolism is an emergent property of sucrose homeostasis. We next demonstrated that hyperbolic function of starch degradation rate that has a peak at dawn is necessary for sucrose homeostasis. We then showed that a phase response curve to sucrose signals that realizes sucrose homeostasis is the same as the one determined by the experiment, which shows phase advance in the morning and delay in the night. We finally showed that the phase response to sucrose signals leads to appropriate adjustment of starch accumulation and degradation rates. These results indicate that the responsiveness of plant circadian clocks to sucrose signals has the adaptive significance for optimal growth under diel and seasonal fluctuations in environments. [mehr]
A. alpina is a Brassicaceae species and perennial relative of the annual model Arabidopsis thaliana. Comparative studies between these two models have been successful in tracing at the molecular level the mechanisms that contributed to the diversification of the annual and perennial life strategies. Differences in flowering behavior between annual and perennial species contribute to differences in their life strategy. A text book example is the role of FLOWERING LOCUS (FLC) in life history evolution of A. alpina and A. thaliana. FLOWERING LOCUS C (FLC) is a key floral repressor in A. thaliana that regulates flowering in response to vernalisation. Its orthologue in A. alpina, PERPETUAL FLOWERING 1 (PEP1) also ensures flowering in response to vernalisation but in addition contributes to perennial traits such as polycarpic growth habit and the duration of the flowering episode. pep1 mutants flower without vernalisation and show reduced return to vegetative growth. My group is studying the regulation of inflorescence development and outgrowth in perennials using A. alpina as a model. We performed an enhancer screen of the pep1-1 mutant and isolated several second-site mutants that show inflorescence phenotypes. Mapping by sequencing of several mutants reveal a novel regulator not previously studied in A. thaliana. [mehr]
Bacterial microcompartments are widespread metabolic modules found in at least 23 bacterial phyla. The carboxysome is the best studied bacterial microcompartment and serves to illustrate the basic principles of bacterial micrcompartment structure and function. It consists of a selectively permeable protein shell encapsulating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. Cyanobacteria depend on the carboxysome to concentrate carbon dioxide near RuBisCO while minimizing the wasteful side reaction with oxygen. The carboxysome functions as an organelle but, in contrast to eukaryotic organelles, is composed entirely of protein; thousands of protein subunits self-assemble to form this ~300 MDa complex. Many bacteria assemble architecturally-related types of organelles for diverse catabolic functions. Our studies suggest that the principles of carboxysome structure, function and assembly likely extend to other bacterial microcompartments and provide the foundation for design and construction of synthetic nanoreactors based on bacterial microcompartment architecture. [mehr]
In plants and animals, induced resistance (IR) to biotic and abiotic stress is associated with priming of cells for faster and stronger activation of defense responses. Cell priming involves accumulation of latent signaling components that are not used until challenge exposure to stress. During development of induced resistance in Arabidopsis thaliana, priming is associated with accumulation of mRNA and inactive proteins of mitogen-activated protein kinases (MPKs), MPK3 and MPK6. Upon challenge exposure to biotic or abiotic stress, these two enzymes are more strongly activated in primed plants than in nonprimed plants. This elevated activation is linked to enhanced defense gene expression and development of IR. Because the identity of most in vivo MPK target proteins remained elusive, we developed a robust and powerful method to identify and quantify site-specific phosphorylation of low-abundant MPK substrates on a large scale. Our approach represents a two-step chromatographic procedure combining phosphoprotein enrichment using Al(OH)3-based metal oxide affinity chromatography (MOAC), tryptic digest of enriched phosphoproteins, and TiO2-based MOAC to enrich phosphopeptides. When applied to transgenic conditional gain-of-function Arabidopsis plants supporting in planta activation of MPKs, the tandem-MOAC approach allows direct measurement and quantification ex vivo of site-specific phosphorylation of several reported and many so far unknown, MPK substrates in a single experiment. [mehr]
Cell-cell-communication is essential for multicellular development and consequently, evolution has brought about an array of distinct mechanisms serving this purpose. Consistently, induction and maintenance of stem cell fate by non-cell autonomous signals is a feature shared by many organisms and may depend on secreted factors, direct cell-cell contact, matrix interactions, or a combination of these mechanisms. While many basic cellular processes are well conserved between animals and plants, cell-to-cell signaling is one function where substantial diversity has arisen between the two kingdoms of life. One of the most striking differences is the presence of cytoplasmic bridges, called plasmodesmata, which facilitate the exchange of molecules between neighboring plant cells and provide a unique route for cell-cell communication in the plant lineage. Here we provide evidence that the stem cell inducing transcription factor WUSCHEL (WUS), expressed in the niche, moves to the stem cells via plasmodesmata in a highly regulated fashion and that this movement is required for WUS function and thus stem cell activity in Arabidopsis thaliana. We show that cell context independent mobility is encoded in the WUS protein sequence and mediated by multiple domains. Finally, we demonstrate that parts of the protein that restrict movement are required for WUS homo-dimerization, suggesting that formation of WUS dimers might contribute to the regulation apical stem cell activity. [mehr]

Markus Schmid - Integration of Flowering Time in Arabidopsis thaliana

April 2016
The induction of flowering is a central event in the life cycle of plants. When timed correctly, it helps ensure reproductive success, and therefore has adaptive and economic value: precocious flowering often results in reduced yield, both in biomass and fruits, whereas a delay in flowering can result in an increase of biomass. However, the latter is usually accompanied by reduced seed set or seed filling, limiting the use of late-flowering varieties in agronomics. Because of its importance, flowering is under the control of a complex genetic circuitry that integrates endogenous signals such as hormonal and carbohydrate status, and environmental signals such as temperature and light. Genetic analyses had initially suggested the existence of genetically defined pathways that regulate flowering in response to a specific input. Over the last several years, however, it has become apparent that many important flowering time genes are not regulated by single inputs, but rather integrate multiple, often contradictory signals to control the induction of flowering. I will discuss our recent findings on different flowering time pathways in Arabidopsis thaliana and dynamic changes of the chromatin landscape at the shoot apical meristem during the floral transition. [mehr]
Much of biology is associated with the evolution of convergent traits. For example the eyes of squids and squirrels have evolved independently by harnessing the same genes and developmental pathways. However convergent evolution also occurs at smaller scales and can be seen in thousands of examples of how organisms adapt their genes and genomes to respond to the shared challenges of survival. In this talk I will discuss how studying the parallel evolution of new genes has provided new insight into the evolution of C4 photosynthesis. I will then discuss how adaptation to changes in metabolism can drive the parallel evolution of genomes. [mehr]

Thilo Rühle - Assembly of chloroplast F1F0–ATP synthases

March 2016
F1F0-ATP synthases are multiprotein complexes, which are found in all living organisms. They meet the cellular demand for ATP and maintain ion gradients across membranes by an ion-flux-dependent, reversible ATP synthesis/hydrolysis reaction. Bacterial, mitochondrial and chloroplast F1F0-ATP synthases share the same core structure: a soluble F1 domain responsible for reversible ATP generation is connected by two stalks to the ion-translocating membrane domain. Correct assembly of F1F0-ATP synthases depends on multiple, intertwined cellular processes, and is even more challenging in eukaryotic organelles, since here – in addition to tight regulation of subunit transcription and translation – coordination of organellar import processes and two protein synthesis machineries is essential. Thus, biogenesis of F1Fo-ATP synthases requires the intervention of auxiliary factors, which carry out specialized functions in this highly concerted process. In a search for novel photosynthesis-relevant factors in Arabidopsis thaliana, proteins were considered that are shared by photosynthetic eukaryotes from the green lineage but that are not found in non-photosynthetic eukaryotes. Those proteins are called GreenCut proteins and are likely to be associated with chloroplast functions. Knockout mutant lines were isolated and analyzed with respect to photosynthetic perturbations using a chlorophyll fluorescence screening procedure. As a result, we could identify two GreenCut proteins, which are specifically required for chloroplast F1F0-ATP synthase accumulation and provided evidence that they are involved in chloroplast F1F0-ATP synthase assembly. [mehr]

Javier Agusti - Secondary growth in plants: from models to crops

Multicellular organisms develop by integrating and coordinating multiple growth programs. In plants, a paradigm for such systems is the secondary growth (thickening) of stems and roots. Secondary growth provides the mechanical support and stability that plants need to expand their longitudinal growth, to generate new growth axes in the form of branches and to sustain new structures such as fruits, leaves or flowers. In addition to playing a crucial role in plant development, secondary growth is of relevant social and economic importance. First, in trees, secondary growth brings about wood: one of the largest sources of terrestrial biomass, the largest sink of atmospheric CO2 after oceans and a main source of raw material for the renewable energy, construction, timber, paper or pulp industries. Second, in terms of agriculture, secondary growth is key for determining crop architecture and properties. Secondary growth is the result of the formation of secondary vascular tissues (secondary xylem and secondary phloem). The secondary vascular tissues develop through the activity of a highly specialized pool of stem cells (meristem) termed cambium. In our lab we focus mainly in (i) the genetic regulation of cellular proliferation within the cambium and (ii) the impact of cambium-mediated cell fate determination on organ architecture. We use specific plant species depending on the actual question to be addressed. In my talk I will summarize our work in Arabidopsis thaliana (which we use as an example to study cellular proliferation in the cambium) and in Manihot esculenta (Cassava), which we use as an example to understand the impact of cell fate determination on organ architecture. Due to the social relevance of Cassava, potential applications of our work will be discussed. [mehr]

Torgny Näsholm - Soil Nitrogen Sources and Plant Nitrogen Acquisition

Traditionally, research on plant nitrogen nutrition has had a strong focus on the inorganic nitrogen sources ammonium and nitrate. Their abundance in soils, their rapid uptake and the ease by which they can be used to cultivate plants have constituted a strong motivation for this focus. However, recent studies have emphasised the ubiquitous competence of plants, both mycorrhizal and non-mycorrhizal, to uptake various organic nitrogen sources, in particular amino acids. This raises the fundamental question; what nitrogen sources do plants acquire from soils? We argue that the answer to this question depends on the two fundamental steps in plant nitrogen nutrition: (i) what nitrogen sources are plant roots encountering in the soil and (ii) to what extent are these nitrogen sources absorbed? (i): We have adopted a method, microdialysis, originally developed for monitoring neurotransmitters in rodent brains, to study soil nitrogen dynamics. Microdialysis probes share important characteristics with plant fine roots and allows for low-invasive monitoring of solutes in soil. We argue that soil microdialysis may give important insights regarding the nitrogen sources encountered by roots. Results from in situ microdialysis of soil nitrogen in boreal forests as well as in subtropical sugarcane fields will be discussed. (ii): Several transporters have been implicated as responsible for root uptake of amino acids. The Lysine Histidine Transporter 1 (LHT1) was shown to mediate root uptake of neutral and acidic amino acids by Hirner et al. (2006). Studies in our lab have confirmed the importance of LHT1 for plant amino acid nutrition and also shown that Amino Acid Permease 5 complements LHT1 by mediating uptake of basic amino acids. We have used Arabidopsis LHT1 mutants to examine the importance of amino acids in plant nitrogen nutrition. Results from these studies will be presented. [mehr]

Andreas Weber - Evolution and function of C4 photosynthesis

January 2016
C4 photosynthesis is a remarkable example of convergent evolution of a complex trait. It has independently evolved more than 70-times in monocotyledonous and dicotyledonous flowering plants, including at least two independent origins in the Brassicales. With few exceptions, all C4 plant species display a distinct leaf anatomy called Kranz-anatomy as well as similar metabolic and biochemical features. Using computational modeling, we have shown that C4 photosynthesis evolves from C3 photosynthesis on a smooth upward trajectory via C3-C4 intermediate states (Heckmann et al., 2013). C3-C4 intermediacy evolves via simple loss of function mutations and causes a nitrogen disbalance between leaf mesophyll and bundle sheath cells. Overcoming this nitrogen disbalance requires the shuttling of organic acids between mesophyll and bundle sheath cells, which under permissive conditions sets the system on a slippery slope towards C4 photosynthesis (Mallmann et al., 2014). [mehr]
This seminar was cancelled and postponed to January. The new date will be published as soon as possible. [mehr]

Science Journalism at Laborjournal, Lab Times,... And Elsewhere

There is no standard route for becoming a science writer or science journalist. However, at least in terms of education the vast majority enters science journalism from the science side. This talk will give an overview of how Laborjournal and – later – Lab Times once entered the scene and what exactly have since proven to be the conceptual key elements for their establishment and success. One of these key elements clearly was that Laborjournal and Lab Times right from the start took a couple of different approaches than most other science print media. On the other hand, the constant comparison with other science media has proven very useful in order to identify important key ingredients of having success and fun (!) in the science journalism business in general. Some insights in this regard shall also be shared and discussed in this talk. [mehr]

Translational Dynamics in the Arabidopsis Seed

Seeds are unique living structures that survive being dried to less than 5% water content and are revitalized during germination. Protein translation is required during the early stages of germination prior the need of transcription. Genome-wide profiling of the total mRNA and polysome associated mRNA pools of Arabidopsis seeds identified extensive translation regulation in seeds, specifically during germination. The mechanism and possible relevance of these novel regulatory patterns in seed physiology will be discussed. [mehr]

The Plant Cell in the new age of scientific publishing

The Plant Cell is a premier venue for publication of your best research in plant biology. With a new Editor-in-Chief on board, this year brings many changes to publication and the peer review process. As an online-only journal, there is a flat fee for publication, which includes post-review scientific editing and full color images for technical conformity and visually aesthetic presentation of your data. An expanded board of scientific editors who are encouraged to solicit reviews from a broader community of researchers offers the authors expert review and guidance. The pre-review process involving at least two editors enables expedited decisions so that full-review is restricted to the papers deemed most likely to be approved after peer-review. A post-review discussion between reviewers and multiple editors prior to rendering a decision to the author ensures fair and scholarly appreciation of the authors work. We will make suggestions on how to take advantage of the true peer-review process of The Plant Cell to ensure that your work is reviewed and appreciated by the most appropriate audience. We will also inform you of new initiatives at the journal and what we are doing to advertise your work to the broader community (http://www.plantcell.org/content/27/2/303.full). [mehr]

Circadian control of seasonal rhythms in Arabidopsis

December 2015
Plants respond to seasonal cues in order to anticipate the expected environmental changes that accompany the changing seasons. Well-known examples of seasonal control of development in plants are photoperiodic control of flowering and hypocotyl elongation, both of which are regulated by the circadian clock via the CONSTANS (CO) and PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors, respectively. We recently developed an integrated mathematical model of these pathways, identifying novel signalling dynamics across hundreds of co-regulated transcripts. Beyond these canonical examples of seasonal regulation, we have also identified a general principle of photoperiodic regulation of protein expression. This regulation arises from changes in the timing of bulk protein synthesis with photoperiod. We validated a simple model of this effect using quantitative transcriptomic and proteomic datasets across a range of photoperiods. My ongoing work seeks to identify other aspects of plant physiology that show seasonal responses, and to uncover the molecular mechanisms of these responses. The ongoing proliferation of genome-scale datasets in plant biology means that computational approaches are fast becoming a vital tool for exploring new hypotheses in these diverse contexts. [mehr]
A RecG-like DNA helicase is involved in the surveillance of recombination and segregation of plant organellar genomes Clémentine Wallet, Monique Le Ret, André Dietrich and José Gualberto The plasticity of plant mitochondrial genomes is due to recombination processes that modulate their structure. Several factors have already been identified involved in organellar recombination or in recombination-dependent repair processes. But how the segregation of the alternative mitotypes generated by recombination is controlled, is still not understood. An Arabidopsis gene (RECG1) codes for a homologue of bacterial DNA helicase RecG. In bacteria RecG has multiple roles in DNA repair, the control of stoichiometric genome replication and the suppression of ectopic recombination. The plant RECG1 is dually targeted to mitochondria and plastids and can complement bacterial recG deficient strains for repair and replication control. Arabidopsis recG1 mutants have increased ectopic recombination between intermediate size repeat (IR) in mitochondria, and are deficient in repair of double strand breaks induced by a genotoxic stress. In addition we found that RECG1 has roles in the segregation of mtDNA. In a recG1 line an alternative mtDNA sequence generated by recombination is stably maintained as an independent replisome. Reintegration of the wild type RECG1 allele leads to the segregation of the alternative versions of mtDNA, with individual plants inheriting different mtDNA versions. The precise characterization of the recombination steps involved in this sorting process allowed us to build a model for how it is controlled by RECG1. [mehr]
Many microorganisms accumulate high-energy compounds such as triacylglycerols (TAG) and polyphosphate (polyP) in intracellular granules. These compounds provide energy reserves for the cell to survive suboptimal conditions. Additionally, recent findings have suggested that these high-energy granules are not simply for energy storage, but have important cellular roles involved in protein folding, gene expression and signaling, among others. In addition to understanding the functional significance of these energy reserves, identifying mutants or strains with increased accumulation of TAG or polyP is of biotechnological interest due to our current dependence on non-renewable energy and phosphate sources (i.e. fossil fuel and phosphate mining). In this talk, I will present the use of flow cytometry as a high-throughput screen to detect and enrich for cells hyper-accumulating TAG or polyP. I will first talk about the method we have developed for isolating mutants with increased lipid accumulation in model alga Chlamydomonas reinhardtii. In this approach, 50% of the isolated mutants have a reproducible high lipid phenotype. Secondly, I will present ongoing work on wastewater bacterial community screening for polyP hyper-accumulating strains. Initial findings suggest that bacterial species stemming from phylum Firmicutes and alphaproteobacteria may have a larger role in phosphate removal from wastewater than previously expected. [mehr]

50 Years of Plant Science (1980-2030): Evolution of a research field

November 2015
The evolution of land plants fundamentally changed the earth’s atmosphere and paved the way for terrestrial life as we know it. Despite a pivotal role in both initiating and sustaining animal life, plants received relatively scant attention from biologists for decades. Why? What, if anything, changed? I will discuss my own research trajectory from human genetics to plant developmental genetics, and provide insight into the way in which the research field has changed over the last 35 years. What have we learnt about plant biology, what is left to learn, and what challenges lie ahead? [mehr]
Sunlight is the ultimate energy source driving photosynthesis. In nature, however, absorbed light energy often exceeds the capacity of light utilization in photosynthesis, giving rise to the formation of reactive oxygen species and thus photo-oxidative damage of the chloroplast. Non-photochemical quenching of excitation energy (NPQ) in the antenna of Photosystem II (PSII) allows the harmless dissipation of excess light energy as heat and thereby avoids oxidative damage to the photosynthetic apparatus. Four different mechanisms contribute to NPQ, termed qT, qE, qZ and qI. Under saturating light conditions, the energy dependent-quenching mechanism (qE) represents the dominant NPQ component; qE is based on a complex mechanism which strictly depends on three factors: (i) lumen pH, (ii) the PsbS protein and (iii) the xanthophyll zeaxanthin (Zx). According to the current understanding of qE, a low pH in the thylakoid lumen induces PsbS-dependent conformational changes in the PSII antenna and formation of Zx, both being central for activation of maximum qE capacity. The central role of PsbS in these processes is related to the function of PsbS as sensor of lumenal pH. Our work focuses on the identification of protein interaction partners of PsbS and how these interactions contribute to the pH-regulated reorganization of the PSII antenna during activation of NPQ. Additionally, we are interested in the role of PsbS in green algae as an approach to understand the evolution of photoprotective mechanisms. Altogether, our findings support that throughout land colonization of plants, PsbS evolved as a key player in energy dissipation by modulating light induced protein interactions in the PSII-Antenna required for the activation of qE. [mehr]
Post-translational redox modifications can affect the function of numerous proteins by modulating their activity, their subcellular localization, their stability, or their interactions with partner proteins. Most of these modifications are influenced or controlled by the disulfide reductases thioredoxin (TRX) or glutaredoxin (GRX). The first part of the talk will present evidence for redox regulation of some cytosolic metabolic enymes by TRX or GRX in Arabidopsis. The second part of the talk will present evidence for the crucial role of a multidomain iron-sulfur cluster glutaredoxin GRXS17 in meristem activities and in the response to heat stress. [mehr]
In order to feed an ever-increasing world population, there needs to be a step-change in the way new, more productive varieties are developed. Monitoring of plant growth and composition is being transformed by new imaging methods. Nondestructive measurements mean that individual plants can be followed over time, giving new insights into phenotypic plasticity and developmental change. Focussing on the important crop plants sorghum and cassava, I will present unpublished and published results on how we are using whole plant phenomics and FT-IR and Raman imaging to analyse the costs and benefits of specialised metabolites, focussing on cyanogenic glucosides in Sorghum from our EMS-TILLING population. Ros Gleadow is an ecophysiologist interested in secondary compounds, who has been using the Adelaide phenotyping facility for her work. A recent publication of hers on this is: http://jxb.oxfordjournals.org/content/early/2015/02/18/jxb.eru526.abstract A description of the acyanogenic mutants and the TILLING project can be found here: http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2011.00646.x/abstract [mehr]

Untargeted metabolomics in plant and food research

Metabolomics strategies, and particularly the large-scale untargeted approaches in which all metabolites detected - both known and yet unknown - are taken into consideration, have provided us novel and detailed insights into metabolites and biochemical pathways that are key to traits of plants and products derived thereof. At Plant Research International we focus mostly on accurate mass LCMS, GCTOFMS and GCqMS based untargeted metabolomics techniques, either separately or combined as complementary platforms. In this seminar a few examples of our projects dealing with both technology development and strategic research in (crop) plant and food research will be highlighted. [mehr]

Examining genetics of climatic adaptation in Arabidopsis lyrata

Plant Science Research at Nanyang Technological University Just getting started

October 2015
Nanyang Technological University in Singapore is one of the top ranked universities in the world. Having its roots in engineering NTU in the last 15 years has moved to become a more comprehensive university. This effort has led to the establishment of the School of Biological Sciences in 2001 and the School of Physical and Mathematical Sciences in 2005, the latest addition is the Medical School which was established only three years ago. During the initial phase of the expansion of NTU the biomedical science area had been identified as a key area to focus on, leading to an overall program which is highly focused on medical related areas. NTU and particular the School of Biological Sciences has now come to realize that Plant Science/Biology and its importance not only in food production and Oxygen production but also as a source of novel chemistry will be one of the future growth areas for Singapore. NTU’s unique location within one of the most bio diverse regions of the world as well as the state of the art technology in omic technologies available within Singapore makes it an attractive location for plant science research with a different perspective. The presentation today will focus on the “plant science” research that is already going on today at NTU and highlight some of the technology platforms that already exist. This presentation aims to serve as the basis of a discussion on how the Max Plank Institute and NTU could develop closer ties in an effort to develop a synergistic research program between the two institutions. [mehr]

Genome-wide analyses of translational dynamics in chloroplasts

The translation of chloroplast mRNAs has long been known to be subject to regulation by developmental, environmental and physiological cues. However, progress in recognizing examples of translational regulation, identifying translational regulators, and dissecting mechanisms of translational modulation has been limited by the assays that have been available to monitor ribosome behavior in vivo: the traditional assays (pulse-labeling, polysome, and reporter gene approaches) are labor intensive, have limited sensitivity and/or resolution, and are not suited to genome-wide explorations. We are using genome-wide ribosome profiling methods that provide a quantitative and high resolution readout of ribosome positions in vivo to (i) identify nucleus-encoded proteins that are required for the translation of specific chloroplast mRNAs; (ii) analyze the impact of various light regimes on chloroplast ribosome behavior; (iii) describe the translational dynamics of organellar mRNAs during the differentiation of photosynthetic leaf cells; and (iv) elucidate mechanisms involved in the co-translational targeting of proteins to the chloroplast thylakoid membrane. Examples of insights obtained in each of these areas will be discussed. [mehr]
What makes some clades produce more species than others? The answers may be genetic, genomic, or morphological. This talk will focus on the grass tribe Andropogoneae, an economically and ecologically important group that includes maize, sugarcane, sorghum and Miscanthus. Most species in the clade are polyploid, and we find that allopolyploidy is a predominant mode of speciation in the group. However, the net speciation rate does not increase after polyploidy. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C4 grasslands that dominate the earth today. Morphological characteristics include a distinctive seed dispersal unit derived from a pair of spikelets and the associated inflorescence stalk. This structure is usually assumed to be selected for seed dispersal, but also affects breeding system and the investment into pollen and ovules, and is a source of carbon for the developing grain. Thus the structure of the inflorescence may be under selection for pollination, seed filling, or seed dispersal. This may be as important as repeated allopolyploidy in driving speciation. [mehr]

Chloroplasts – a new effector battleground?

September 2015
Successful pathogens attenuate a battery of sophisticated plant surveillance defences by deploying a collection of “effector” molecules, the majority of which are function redundantly in planta, targeting multiple levels and nodes of an activated innate immune signalling network. We have made remarkable progress towards understanding how molecular patterns of potential pathogens are recognised by pattern recognition receptor complexes at the host-pathogen interface to activate a kinase signalling cascade leading to transcriptional re-programming that underpins plant innate immunity. Early transcriptional events occur within 30 min of Pseudomonas infection, but the pathogen does not multiply until 7-8 hpi. Our knowledge of the core host physiological processes modified by multiple effectors to promote virulence, remains rudimentary. High-resolution microarray time courses of a compatible infection of Arabidopsis with P. syringae pv. tomato DC3000 and the disarmed hrpA mutant combined with genetic, physiological and real-time imaging studies revealed that the chloroplast, a key organelle in primary carbon metabolism and site of synthesis of hormone precursors, is rapidly targeted by bacterial effectors. Within 2hpi of DC3000 or hrpA challenge, ~20% of all differentially suppressed transcripts are nuclear encoded chloroplast targeted genes (NECG) subsequently exceeding 35%. Within 3hpi effectors reprogramme NECG transcription. We show that many effectors have potential chloroplast targeting sequences and these can translocate to chloroplasts, where they attenuate a MAMP activated chloroplast reactive oxygen burst, probably through elevation of ABA. Attenuation of the oxidative burst by exogenous application of DCMU allows growth of the hrpA mutant. This talk with discuss our progress towards understanding chloroplast immunity. [mehr]

Plant growth beyond limits

August 2015
Plant and plant organ growth are regulated by an exceedingly complex interplay of many genes and their interaction with the ever changing environment. The long-term goal of my research is to obtain a holistic understanding of plant organ growth. Numerous genes of which the modified expression enhances plant organ growth have now been identified, and a detailed study of these genes provided novel insights in the molecular machines driving growth. Furthermore, evidence obtained both in the model plant Arabidopsis and in maize, demonstrated that the combination of multiple growth enhancing genes can have very profound effects on organ sizes. Green house and field experiments with transgenic maize also provided very promising results. Tremendous progress has also been made in understanding how environmental cues, such as mild drought stress, negatively affect plant growth. In unpredictable environments, growth reduction enables plants to redistribute and save resources, ensuring reproduction, even when the stress becomes extreme. However, when the episode of stress does not threaten plant survival, and from the agricultural point of view, growth reduction can be seen as counter-productive, leading to unnecessary yield loss. Limiting growth reduction may thus provide a strategy to boost plant productivity under stress. I will discuss how our insights open up new perspectives for the identification of optimal growth regulatory networks that can be selected by advanced breeding, or for which more robust variants (e.g. reduced susceptibility to drought) can be obtained through genetic engineering. The ability to improve growth of maize and, in analogy other cereals, could have a major impact in providing food security. [mehr]
The leaf epidermis is a well-suited tissue to study cell fate acquisition in plants. In the stomatal lineage, stem cell-like meristemoids give rise to pavement cells and stomatal guard cells, which together account for over 80% of leaf epidermal cells. Plant cells polarize and divide asymmetrically in order to achieve two daughter cells with different fates. Two proteins have been identified so far that account for cell polarization in the stomatal lineage. Immediately before cell division, these polarized proteins accumulate in membrane subdomains that are inherited by only one of the two daughter cells. Mutations in the corresponding genes lead to loss of asymmetry with regards to both size and fate of the daughter cells. Mechanisms for cell polarization in the stomatal lineage that integrate the plethora of external signals, including hormones, cell-cell communication and mechanical cues are, as of yet, unknown. My research focuses on the interplay of mechanical and chemical signals, apparent in the leaf epidermis. Inducing artificial changes in the mechanical stress environment through cell ablations and tissue stretching, I could show that polarized proteins change their orientation throughout the tissue. This is coherent with changes of the global orientation of the microtubule cytoskeleton. How these processes are coordinated with each other and tie in with peptide signaling among epidermis cells is part of my ongoing investigation. [mehr]

A framework for Transcriptional Repression in Plants

July 2015

Coevolutionary interactions on two time scales: Bacillus thuringiensis vs Insects

Abstract: Certain strains of the gram-positive soil-dwelling bacterium Bacillus thuringiensis (Bt) produce pore-forming toxins that kill insect larvae and nematodes that ingest them, by attacking targets in the midgut. A signature of this long-term coevolutionary interaction between prokaryotes and eukaryotes can be seen in bacterial strategies to diversify and combine different toxins, and in insect strategies to evade or degrade them. Bt toxins are now widely used in spray formulations and in transgenic crops to control insect pests of human agriculture and human health, presenting the opportunity to examine this coevolutionary interaction on a much shorter timescale. In fact, similar to the situation with chemical insecticides, evolution of Bt resistance by the target pests increasingly threatens their sustainable use in agriculture. We describe case studies of recently-evolved Bt resistance in insects to show how microevolutionary steps, some including humans as agents, can inform our understanding of the macroevolutionary patterns resulting from the toxin arms race. [mehr]

Evolution of a fully functional Calvin cycle in E. coli

Hybridization, adaptation and ecological opportunity

April 2015
Abstract: A fundamental theory of quantitative genetics predicts that the amount of standing genetic variation is crucial to adaptation and the generation of diversity. My research shows that hybridization between distant species instantaneously elevates levels of genetic variation and can lead to adaptive advantages of hybrids under stressful conditions. I used Saccharomyces yeast to generate hybrid populations of vast genetic and phenotypic variation and tested their evolutionary potential under different environmental scenarios. I found that transgressive segregation generates extreme hybrid phenotypes that were between 1.5 and 3-fold fitter than the mid-parent, enabling them to colonize novel environments lethal to parental populations. The extent of hybrid transgression was correlated to the genetic and phenotypic crossing distance between their parents, consistent with the prediction that allelic complementation and/or epistasis in hybrids become more frequent the longer two parental lineages have evolved independently from each other. Using experimental evolution in gradually deteriorating environments, I further show that hybridization can lead to the evolutionary rescue of populations. Hybrids adapted to more degraded environments than non-hybrids, resulting in survival rates far exceeding those of their ancestors. The resilience of populations to habitat degradation is a major concern for biodiversity conservation. My research shows that hybridization can increase evolutionary responsiveness and that taxa able to exchanges genes with distant relatives may better survive rapid environmental change. This may be useful in a world where hybridization is becoming increasingly common due to the relocation of plants and animals by humans. [mehr]

Energy signaling: connecting environmental stress and plant growth

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