Current status of the plant phosphorylation site database PhosPhAt and its use as a resource for molecular plant physiology

As the most studied post-translational modification, protein phosphorylation is analyzed in a growing number of proteomic experiments. These high-throughput approaches generate large datasets, from which specific spectrum-based information can be hard to find. In 2007, the PhosPhAt database was launched to collect and present Arabidopsis phosphorylation sites identified by mass spectrometry from and for the scientific community. At present, PhosPhAt 3.0 consolidates phosphoproteomics data from 19 published proteomic studies. Out of 5460 listed unique phosphoproteins, about 25% have been identified in at least two independent experimental setups. This is especially important when considering issues of false positive and false negative identification rates and data quality (Durek etal., 2010). This valuable data set encompasses over 13205 unique phosphopeptides, with unambiguous mapping to serine (77%), threonine (17%), and tyrosine (6%). Sorting the functional annotations of experimentally found phosphorylated proteins in PhosPhAt using Gene Ontology terms shows an over-representation of proteins in regulatory pathways and signaling processes. A similar distribution is found when the PhosPhAt predictor, trained on experimentally obtained plant phosphorylation sites, is used to predict phosphorylation sites for the Arabidopsis genome. Finally, the possibility to insert a protein sequence into the PhosPhAt predictor allows species independent use of the prediction resource. In practice, PhosPhAt also allows easy exploitation of proteomic data for design of further targeted experiments

Use of phenotyping technologies in improving plant performance under abiotic stress, focusing on plant nutrient uptake and interaction with beneficial microbes

Non-invasive phenotyping allows the quantification of plant growth parameters without affecting the observed individuals. As such it opens possibilities for temporal studies of growth rates and development of root and shoot architecture and linking these to the underlying molecular changes (phenomics).In the root dynamics group we link time and RSA from the moment of plant inoculation with a microorganism, to study the plant-microbe interaction (Sanow et al., 2023). To do so we use a number of platforms. We are in close collaboration with the Julich plant phenotyping center, where we often have to make standard operating protocols applicable with microbial inoculation.The shoot and root system architectural (RSA) response through time is crucial for determining e.g., the necessary time from inoculation to quantifiable plant recovery of a stress phenotype and selecting timepoints for invasive harvest for molecular approaches (often transcript, metabolite, or protein profiling). In this manner we link abiotic and biotic components in an experimental matrix, which brings us closer to studying the plant edaphic enviroment which is crucial for later application.In my talk I will describe the use of gnotobiotic systems like the EcoFab (Kuang et al., 2022, Mau et al., 2022), semi-controlled systems like the Grow Screen Agar (Macabuhay et al., 2022), GrowScreen-Page (Schilacci et al., 2020, 2021) used in the study of plant-microbe interactions. I will show the progression to green-house (soil-) based systems for shoot and root Phenotyping (Screen-house and Rhizotrons) and will inform the audience about additional phenotyping work in the IBG-2 Plant Sciences

The molecular basis of zinc homeostasis in cereals

Plants require zinc (Zn) as an essential cofactor for diverse molecular, cellular and physiological functions. Zn is crucial for crop yield, but is one of the most limiting micronutrients in soils. Grasses like rice, wheat, maize, and barley are crucial sources of food and nutrients for humans. Zn deficiency in these species therefore not only reduces annual yield but also directly results in Zn malnutrition of more than two billion people in the world. There has been good progress in understanding Zn homeostasis and Zn deficiency mechanisms in plants. However, our current knowledge in monocots, including grasses, remains insufficient. In this review, we provide a summary of our knowledge on molecular Zn homeostasis mechanisms in monocots, with a focus on important grass crops. We additionally highlight divergences in Zn homeostasis of monocots and the dicot model Arabidopsis thaliana, as well as important gaps in our knowledge that need to be addressed in future research on Zn homeostasis in cereal monocots

Service for controlling household electrical devices through the internet

This paper provides description of service which offers controlling household electrical devices through the Internet, remotely. The concept of the service in this format is designed as a student’s project and it gives the basic idea which can be improved. At the beginning, importance of the problem of electrical energy consumption is explained. Some illustrative examples for improving energy consumption of the devices are given. The idea of IoT (Internet of Things) internetworking is analyzed as potential solution for the problem. Our service is based on the IoT and it is combination of some simple hardware and software components which are specified and explained separately. The business potential of developing service of this kind is mentioned. Finally, we summarize the benefits that users can obtain by implementing this system in their households

The molecular basis of zinc homeostasis in cereals.

peer reviewedPlants require zinc (Zn) as an essential cofactor for diverse molecular, cellular and physiological functions. Zn is crucial for crop yield, but is one of the most limiting micronutrients in soils. Grasses like rice, wheat, maize and barley are crucial sources of food and nutrients for humans. Zn deficiency in these species therefore not only reduces annual yield but also directly results in Zn malnutrition of more than two billion people in the world. There has been good progress in understanding Zn homeostasis and Zn deficiency mechanisms in plants. However, our current knowledge of monocots, including grasses, remains insufficient. In this review, we provide a summary of our knowledge of molecular Zn homeostasis mechanisms in monocots, with a focus on important cereal crops. We additionally highlight divergences in Zn homeostasis of monocots and the dicot model Arabidopsis thaliana, as well as important gaps in our knowledge that need to be addressed in future research on Zn homeostasis in cereal monocots

Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics

Protein posttranslational modifications (PTMs) are among the fastest and earliest of plant responses to changes in the environment, making the mechanisms and dynamics of PTMs an important area of plant science. One of the most studied PTMs is protein phosphorylation. This review summarizes the use of targeted proteomics for the elucidation of the biological functioning of plant PTMs, and focuses primarily on phosphorylation. Since phosphorylated peptides have a low abundance, usually complex enrichment protocols are required for their research. Initial identification is usually performed with discovery phosphoproteomics, using high sensitivity mass spectrometers, where as many phosphopeptides are measured as possible. Once a PTM site is identified, biological characterization can be addressed with targeted proteomics. In targeted proteomics, Selected/Multiple Reaction Monitoring (S/MRM) is traditionally coupled to simple, standard protein digestion protocols, often omitting the enrichment step, and relying on triple-quadruple mass spectrometer. The use of synthetic peptides as internal standards allows accurate identification, avoiding cross-reactivity typical for some antibody based approaches. Importantly, internal standards allow absolute peptide quantitation, reported down to 0.1 femtomoles, also useful for determination of phospho-site occupancy. S/MRM is advantageous in situations where monitoring and diagnostics of peptide PTM status is needed for many samples, as it has faster sample processing times, higher throughput than other approaches, and excellent quantitation and reproducibility. Furthermore, the number of publicly available data-bases with plant PTM discovery data is growing, facilitating selection of modified peptides and design of targeted proteomics workflows. Recent instrument developments result in faster scanning times, inclusion of ion-trap instruments leading to parallel reaction monitoring- which further facilitates S/MRM experimental design. Finally, recent combination of data independent and data dependent spectra acquisition means that in addition to anticipated targeted data, spectra can now be queried for unanticipated information. The potential for future applications in plant biology is outlined