Katja Baerenfaller

Publications (18) View all

• Source

  Available from: Katja Baerenfaller

  Article: Common and specific protein accumulation patterns in different albino/pale green (apg) mutants reveals regulon organization at the proteome level.

  Reiko Motohashi, Anja Rödiger, Birgit Agne, Katja Baerenfaller, Sacha Baginsky
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  ABSTRACT: Research interest in proteomics is increasingly shifting towards the reverse genetic characterization of gene function at the proteome level. In plants, several distinct gene defects perturb photosynthetic capacity resulting in the loss of chlorophyll and an albino or pale green phenotype. Because photosynthesis is interconnected with the entire plant metabolism and its regulation, all albino plants share common characteristics that are determined by the switch from autotrophic to heterotrophic growth. Reverse genetic characterizations of such plants often cannot distinguish between specific consequences of a gene defect from generic effects in response to perturbations in photosynthetic capacity. Here we set out to define common and specific features of protein accumulation in three different albino/pale green (APG) plant lines. Using quantitative proteomics we report a common molecular phenotype that connects the loss of photosynthetic capacity with other chloroplast and cellular functions, such as protein folding and stability, plastid protein import and the expression of stress-related genes. Surprisingly, we do not find significant differences in the expression of key transcriptional regulators suggesting that substantial regulation occurs at the posttranscriptional level. We examine the influence of different normalization schemes on the quantitative proteomics data and report all identified proteins along with their fold-changes and p-values in albino plants in comparison to wild type. Our analysis provides an initial guidance for the distinction between general and specific adaptations of the proteome in photosynthesis-impaired plants.
  Plant physiology 10/2012; · 6.53 Impact Factor
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  Available from: Katja Baerenfaller

  Article: Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit.

  Katja Baerenfaller, Catherine Massonnet, Sean Walsh, Sacha Baginsky, Peter Bühlmann, Lars Hennig, Matthias Hirsch-Hoffmann, Katharine A Howell, Sabine Kahlau, Amandine Radziejwoski, [......], Dorothea Rutishauser, Ian Small, Daniel Stekhoven, Ronan Sulpice, Julia Svozil, Nathalie Wuyts, Mark Stitt, Pierre Hilson, Christine Granier, Wilhelm Gruissem
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  ABSTRACT: Leaves have a central role in plant energy capture and carbon conversion and therefore must continuously adapt their development to prevailing environmental conditions. To reveal the dynamic systems behaviour of leaf development, we profiled Arabidopsis leaf number six in depth at four different growth stages, at both the end-of-day and end-of-night, in plants growing in two controlled experimental conditions: short-day conditions with optimal soil water content and constant reduced soil water conditions. We found that the lower soil water potential led to reduced, but prolonged, growth and an adaptation at the molecular level without a drought stress response. Clustering of the protein and transcript data using a decision tree revealed different patterns in abundance changes across the growth stages and between end-of-day and end-of-night that are linked to specific biological functions. Correlations between protein and transcript levels depend on the time-of-day and also on protein localisation and function. Surprisingly, only very few of >1700 quantified proteins showed diurnal abundance fluctuations, despite strong fluctuations at the transcript level.
  Molecular Systems Biology 08/2012; 8:606. · 8.63 Impact Factor
• Source

  Available from: Emøke Bendixen

  Article: The HUPO initiative on Model Organism Proteomes, iMOP.

  Alexandra M E Jones, Ruedi Aebersold, Christian H Ahrens, Rolf Apweiler, Katja Baerenfaller, Mark Baker, Emøke Bendixen, Steve Briggs, Philip Brownridge, Erich Brunner, [......], Lennart Martens, Christian Ravnsborg, Sabine P Schrimpf, Yhong-Hee Shim, Deni Subasic, Andreas Tholey, Klaas van Wijk, Christian von Mering, Manuel Weiss, Xue Zheng
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  ABSTRACT: The community working on model organisms is growing steadily and the number of model organisms for which proteome data are being generated is continuously increasing. To standardize efforts and to make optimal use of proteomics data acquired from model organisms, a new Human Proteome Organisation (HUPO) initiative on model organism proteomes (iMOP) was approved at the HUPO Ninth Annual World Congress in Sydney, 2010. iMOP will seek to stimulate scientific exchange and disseminate HUPO best practices. The needs of model organism researchers for central databases will be better represented, catalyzing the integration of proteomics and organism-specific databases. Full details of iMOP activities, members, tools and resources can be found at our website http://www.imop.uzh.ch/ and new members are invited to join us.
  Proteomics 02/2012; 12(3):340-5. · 4.43 Impact Factor
• Article: Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.

  Sonja Reiland, Gaëlle Messerli, Katja Baerenfaller, Bertran Gerrits, Anne Endler, Jonas Grossmann, Wilhelm Gruissem, Sacha Baginsky
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  ABSTRACT: We have characterized the phosphoproteome of Arabidopsis (Arabidopsis thaliana) seedlings using high-accuracy mass spectrometry and report the identification of 1,429 phosphoproteins and 3,029 unique phosphopeptides. Among these, 174 proteins were chloroplast phosphoproteins. Motif-X (motif extractor) analysis of the phosphorylation sites in chloroplast proteins identified four significantly enriched kinase motifs, which include casein kinase II (CKII) and proline-directed kinase motifs, as well as two new motifs at the carboxyl terminus of ribosomal proteins. Using the phosphorylation motifs as a footprint for the activity of a specific kinase class, we connected the phosphoproteins with their putative kinases and constructed a chloroplast CKII phosphorylation network. The network topology suggests that CKII is a central regulator of different chloroplast functions. To provide insights into the dynamic regulation of protein phosphorylation, we analyzed the phosphoproteome at the end of day and end of night. The results revealed only minor changes in chloroplast kinase activities and phosphorylation site utilization. A notable exception was ATP synthase beta-subunit, which is found phosphorylated at CKII phosphorylation sites preferentially in the dark. We propose that ATP synthase is regulated in cooperation with 14-3-3 proteins by CKII-mediated phosphorylation of ATP synthase beta-subunit in the dark.
  Plant physiology 05/2009; 150(2):889-903. · 6.53 Impact Factor
• Article: Persistent mismatch repair deficiency following targeted correction of hMLH1.

  M B Weiss, M I Vitolo, K Baerenfaller, G Marra, B H Park, K E Bachman
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  ABSTRACT: The use of gene therapy to correct mutated or lost gene function for the treatment of human cancers has been an active, yet problematic area of biomedical research. Many technical difficulties, including efficient tissue-specific delivery, integration site specificity and general toxicity, are being addressed. Little is known, however, about the genetic and phenotypic stability that accompanies a successful gene-specific targeting event in a cancer cell. This question was addressed following the creation of a colon cancer cell line in which a mutated hMLH1 gene was corrected via targeted homologous recombination. This correction resulted in the expression of wild-type hMLH1 protein, restoration of the hPMS2 protein and mismatch repair (MMR) proficiency. One of two hMLH1-corrected clones, however, was found to retain defects in MMR activity. These cells continued to express the corrected hMLH1 protein, but had lost expression of another MMR protein, hMSH6. DNA sequence analysis of the hMSH6 gene revealed biallelic expansions of a cytosine repeat region in exon 5 that result in frameshifts leading to premature stop codons. These findings suggest that, similar to acquired drug resistance, the presence of genetically heterogeneous cancer cell populations or acquisition of compensatory mutations can result in 'resistance' to gene replacement therapy.
  Cancer Gene Therapy 02/2007; 14(1):98-104. · 2.80 Impact Factor