TY - JOUR A1 - Hummel, Jan A1 - Keshvari, N. A1 - Weckwerth, Wolfram A1 - Selbig, Joachim T1 - Species-specific analysis of protein sequence motifs using mutual information N2 - Background: Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences. Results: We describe the tool PROfile analysis based on Mutual Information (PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-independence is achieved by generally applied internet delivery standards. As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool. Conclusion: The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences. It is available at http:// promi.mpimpgolm. mpg.de where additional documentation can be found Y1 - 2005 SN - 1471-2105 ER - TY - JOUR A1 - Nukarinen, Ella A1 - Nägele, Thomas A1 - Pedrotti, Lorenzo A1 - Wurzinger, Bernhard A1 - Mair, Andrea A1 - Landgraf, Ramona A1 - Börnke, Frederik A1 - Hanson, Johannes A1 - Teige, Markus A1 - Baena-Gonzalez, Elena A1 - Dröge-Laser, Wolfgang A1 - Weckwerth, Wolfram T1 - Quantitative phosphoproteomics reveals the role of the AMPK plant ortholog SnRK1 as a metabolic master regulator under energy deprivation JF - Scientific reports N2 - Since years, research on SnRK1, the major cellular energy sensor in plants, has tried to define its role in energy signalling. However, these attempts were notoriously hampered by the lethality of a complete knockout of SnRK1. Therefore, we generated an inducible amiRNA:: SnRK1 alpha 2 in a snrk1 alpha 1 knock out background (snrk1 alpha 1/alpha 2) to abolish SnRK1 activity to understand major systemic functions of SnRK1 signalling under energy deprivation triggered by extended night treatment. We analysed the in vivo phosphoproteome, proteome and metabolome and found that activation of SnRK1 is essential for repression of high energy demanding cell processes such as protein synthesis. The most abundant effect was the constitutively high phosphorylation of ribosomal protein S6 (RPS6) in the snrk1 alpha 1/alpha 2 mutant. RPS6 is a major target of TOR signalling and its phosphorylation correlates with translation. Further evidence for an antagonistic SnRK1 and TOR crosstalk comparable to the animal system was demonstrated by the in vivo interaction of SnRK1 alpha 1 and RAPTOR1B in the cytosol and by phosphorylation of RAPTOR1B by SnRK1 alpha 1 in kinase assays. Moreover, changed levels of phosphorylation states of several chloroplastic proteins in the snrk1 alpha 1/alpha 2 mutant indicated an unexpected link to regulation of photosynthesis, the main energy source in plants. Y1 - 2016 U6 - https://doi.org/10.1038/srep31697 SN - 2045-2322 VL - 6 SP - 10248 EP - 10252 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Morgenthal, Katja A1 - Weckwerth, Wolfram A1 - Steuer, Ralf T1 - Metabolomic networks in plants : transitions from pattern recognition to biological interpretation N2 - Nowadays techniques for non-targeted metabolite profiling allow for the generation of huge amounts of relevant data essential for the construction of dynamic metabolomic networks. Thus, metabolomics, besides transcriptomics or proteomics, provides a major tool for the characterization of postgenomic processes. In this work, we introduce comparative correlation analysis as a complementary approach to characterize the physiological states of various organs of diverse plant species with focus on specific participation of metabolites in different reaction networks. The correlations observed are induced by diminutive fluctuations in environmental conditions, which propagate through the system and induce specific patterns depending on the genomic background. In order to examine this hypothesis, numeric examples of such fluctuations are computed and compared with experimentally obtained metabolite data. Y1 - 2006 UR - http://www.sciencedirect.com/science/journal/03032647 U6 - https://doi.org/10.1016/j.biosystems.2005.05.017 ER - TY - JOUR A1 - Höhenwarter, Wolfgang A1 - Larhlimi, Abdelhalim A1 - Hummel, Jan A1 - Egelhofer, Volker A1 - Selbig, Joachim A1 - van Dongen, Joost T. A1 - Wienkoop, Stefanie A1 - Weckwerth, Wolfram T1 - MAPA Distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber JF - Journal of proteome research N2 - Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000,proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date. KW - comparative proteomics KW - mass accuracy KW - protein isoforms KW - potato tuber KW - lipoxygenase KW - protease inhibitor KW - phenotype KW - genetic variability Y1 - 2011 U6 - https://doi.org/10.1021/pr101109a SN - 1535-3893 VL - 10 IS - 7 SP - 2979 EP - 2991 PB - American Chemical Society CY - Washington ER - TY - THES A1 - Weckwerth, Wolfram T1 - Development and applications of mass spectrometric techniques in plant physiology, biochemistry and systems biology : quantifying the molecular phenotype Y1 - 2006 CY - Potsdam ER - TY - GEN A1 - Durek, Pawel A1 - Schudoma, Christian A1 - Weckwerth, Wolfram A1 - Selbig, Joachim A1 - Walther, Dirk T1 - Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins N2 - Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results: We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion: While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structurebased P-site prediction method has been made available at http://phos3d.mpimp-golm.mpg.de. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 141 KW - Support vector machines KW - Microarray data KW - Docking interactions KW - Signal-transduction KW - Sequence alignment Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45129 ER -