BackgroundProtein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites.ResultsFrom the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented.These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected.ConclusionsWe analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future.

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text-based retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.

Using investigations of the spectral dependence of photoconductivity and of the influence of oxygen on photoconductivity a method is developed to test the properties of spacecharge layers a t the surface of CdS, a t least in some extreme cases. The surface spacecharge layer of thick CdS platelets with a photoconductivity greatly sensitive to an oxygen atmosphere is found to be of accumulation type. This makes a re-interpretation necessary of the models so far accepted for the chemisorption and desorption processes. As their ratelimiting steps the direct capture of electrons and holes by neutral and negatively charged oxygen, respectively, is assumed. Theoretical calculations on the basis of this model show qualitative agreement with the experimental results, but desorption seems to be a process more complex than pure photodesorption.Es wird eine Methode entwickelt, die es gestattet, aus der spektralen Verteilung der Photoleitfahigkeit und aus der GroBe des Sauerstoffeinflusses auf die Photoleitfahigkeit den Charakter von Raumladungsrandschichten an der Oberflache von CdS-artigen Photoleitern zu bestimmen. Es zeigt sich, daB an der Oberflache dickerer CdS-Plattchen, deren Photoleitfahigkeit empfindlich gegen Anderungen des Sauerstoffdruckes ist, Anreicherungsrandschichten vorhanden sind. Das macht es notwendig, die bisherigen Modellvorstellungen uber die Chemisorption und Desorption, die wesentlich auf der Annahme von Verarmungsrandschichten beruhen, so abzuandern, daB der geschwindigkeitsbestimmende Teilschritt der Chemisorption bzw. Desorption direkt der Einfang von Elektronen bzw. Lochern durch neutralen bzw. negativ geladenen Sauerstoff ist. Theoretische Berechnungen der zeitlichen Anderung der Photoleitfahigkeit bei Chemisorption und Desorption und der Abhangigkeit dcr Photoleitfahigkeit vom Sauerstoffdruck auf der Grundlage eines so abgeanderten Modells ergeben qualitativ Ubereinstimmung mit den experimentellen Ergebnissen. Ein quantitativer Vergleich fur den Fall der Desorption 1aBt vermuten, daB die Desorption ein konp!izierterer ProzeB als bloBe Photodesorption ist.

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyse and visualise primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e., genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralised Gene GreenCard allows visualising ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from potato and barley, and 2DE-gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic profiling data can be visualised through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.