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Alternative splicing tends to involve protein phosphorylation sites

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Posttranslationally modified amino acids are chemically distinct types of amino acids and in terms of evolution they might behave differently from their non-modified counterparts. In order to check this possibility, we reconstructed the evolutionary history of phosphorylated serines in several groups of organisms. Comparisons of substitution vectors have revealed some significant differences in the evolution of modified and corresponding non-modified amino acids. In particular, phosphoserines are more frequently substituted to aspartate and glutamate, compared to non-phosphorylated serines. Reviewers This article was reviewed by Arcady Mushegian and Sandor Pongor.
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The reversible phosphorylation of proteins regulates almost all aspects of cell life, while abnormal phosphorylation is a cause or consequence of many diseases. Mutations in particular protein kinases and phosphatases gives rise to a number of disorders and many naturally occurring toxins and pathogens exert their effects by altering the phosphorylation states of intracellular proteins. In this lecture, I present an overview of the progress that is being made in developing specific inhibitors of protein kinases for the treatment of cancer and chronic inflammatory diseases and describe how recent advances in our understanding of the specificity and regulation of one particular protein kinase (GSK3) may facilitate the development of drugs to treat diabetes that would not have the potential to be oncogenic. I also discuss the exploitation of specific protein kinase inhibitors for the study of cell signalling and make recommendations for their effective use in cell-based assays.
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The reversible phosphorylation of proteins regulates almost all aspects of cell life, while abnormal phosphorylation is a cause or consequence of many diseases. Mutations in particular protein kinases and phosphatases gives rise to a number of disorders and many naturally occurring toxins and pathogens exert their effects by altering the phosphorylation states of intracellular proteins. In this lecture, I present an overview of the progress that is being made in developing specific inhibitors of protein kinases for the treatment of cancer and chronic inflammatory diseases and describe how recent advances in our understanding of the specificity and regulation of one particular protein kinase (GSK3) may facilitate the development of drugs to treat diabetes that would not have the potential to be oncogenic. I also discuss the exploitation of specific protein kinase inhibitors for the study of cell signalling and make recommendations for their effective use in cell-based assays.
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Protein phosphorylation affects most, if not all, cellular activities in eukaryotes and is essential for cell proliferation and development. An estimated 30% of cellular proteins are phosphorylated, representing the phosphoproteome, and phosphorylation can alter a protein's function, activity, localization and stability. Recent studies for large-scale identification of phosphosites using mass spectrometry are revealing the components of the phosphoproteome. The development of new tools, such as kinase assays using modified kinases or protein microarrays, enables rapid kinase substrate identification. The dynamics of specific phosphorylation events can now be monitored using mass spectrometry, single-cell analysis of flow cytometry, or fluorescent reporters. Together, these techniques are beginning to elucidate cellular processes and pathways regulated by phosphorylation, in addition to global regulatory networks.
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EDAS, a database of alternatively spliced human genes, contains data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. The database is accessible at http://www.gene-bee.msu.ru/edas/.
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Cell signaling mechanisms often transmit information via posttranslational protein modifications, most importantly reversible protein phosphorylation. Here we develop and apply a general mass spectrometric technology for identification and quantitation of phosphorylation sites as a function of stimulus, time, and subcellular location. We have detected 6,600 phosphorylation sites on 2,244 proteins and have determined their temporal dynamics after stimulating HeLa cells with epidermal growth factor (EGF) and recorded them in the Phosida database. Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF, and these were classified by their temporal profiles. Surprisingly, a majority of proteins contain multiple phosphorylation sites showing different kinetics, suggesting that they serve as platforms for integrating signals. In addition to protein kinase cascades, the targets of reversible phosphorylation include ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different transcriptional regulators. The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation.
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Alternative splicing appears to be sciences' pessimist as nothing can reliably be identified along with its many other fundamental problems. On the brighter side, an optimism can still be seen as the splicing's noise provides material for selection of new and beneficial variants. The evolution of alternative splicing may allow various stages be fixed in different species. Specifically, the prevalence and function of alternative splicing is discussed. In addition, several other topics discussed include the evolution of exon-intron structure, the evolution of the alternative exon-intron structure and the functionality of nonconserved isoforms, the origin of alternative regions, the changes in alternative splicing after gene duplication, and lastly, the recognition of alternative exons and databases of alternative splicing.