Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns.

Lysine acetylation is a major posttranslational modification involved in a broad array of physiological functions. Here, we provide an organ-wide map of lysine acetylation sites from 16 rat tissues analyzed by high-resolution tandem mass spectrometry. We quantify 15,474 modification sites on 4,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle contraction. Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity.

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.

Deregulated cellular signalling is a common hallmark of disease, and delineating tissue phosphoproteomes is key to unravelling the underlying mechanisms. Here we present the broadest tissue catalogue of phosphoproteins to date, covering 31,480 phosphorylation sites on 7,280 proteins quantified across 14 rat organs and tissues. We provide the data set as an easily accessible resource via a web-based database, the CPR PTM Resource. A major fraction of the presented phosphorylation sites are tissue-specific and modulate protein interaction networks that are essential for the function of individual organs. For skeletal muscle, we find that phosphotyrosines are over-represented, which is mainly due to proteins involved in glycogenolysis and muscle contraction, a finding we validate in human skeletal muscle biopsies. Tyrosine phosphorylation is involved in both skeletal and cardiac muscle contraction, whereas glycogenolytic enzymes are tyrosine phosphorylated in skeletal muscle but not in the liver. The presented phosphoproteomic method is simple and rapid, making it applicable for screening of diseased tissue samples.

An automatic procedure for evaluation of single cell motility.

BACKGROUND: Cell motility is vital in many physiological and pathological processes, such as embryogenesis, inflammation, wound healing, and metastasis. However, the time-consuming step in the evaluation of individual cell motility is the analysis of hundreds of recorded images of cell cultures in general consisting of retrieving images, one at a time, and marking the positions of individual cells by a computer mouse. Therefore, the aim of the present study was to develop a novel automatic procedure for the evaluation of cell motility. MATERIALS AND METHODS: The procedure was tested on fibroblasts and glioma and adenocarcinoma cells engineered to express the green fluorescent protein by either transient transfection or adenovirus transduction, allowing automatic recognition of cell coordinates on retrieved images. RESULTS: The effects of serum growth factors, teratogenic compounds, and overexpression of transcription factors on the motile behavior of cultured cells were determined. Cell motility was estimated by both manual and automatic marking of cell position and subsequently motility parameters were computed. The results obtained by the two procedures were found to correlate significantly. CONCLUSIONS: We developed a procedure allowing automatic video recording of sparsely seeded cells transfected with a plasmid or tranduced with a recombinant virus expressing the enhanced green fluorescent protein (EGFP).