Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units 英文参考文献.docVIP

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Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units 英文参考文献.doc

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Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units 英文参考文献

DifferentialUseofSignalPeptidesand MembraneDomainsIsaCommonOccurrence intheProteinOutputofTranscriptionalUnits Melissa J.Davis1,Kelly A.Hanson1,Francis Clark1,2,J.Lynn Fink1,Fasheng Zhang1,Takeya Kasukawa3,Chikatoshi Kai3, Jun Kawai3,4,Piero Carninci3,4,Yoshihide Hayashizaki3,4,Rohan D.Teasdale1* 1 Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland, Australia, 2 Advanced Computational Modeling Centre,UniversityofQueensland,St.Lucia,Queensland,Australia,3GenomeExplorationResearchGroup(GenomeNetworkProjectCoreGroup),RIKENGenomicSciences Center,RIKENYokohamaInstitute,Yokohama,Japan,4GenomeScienceLaboratory,DiscoveryResearchInstitute,RIKENWakoInstitute,Wako,Japan Membraneorganizationdescribestheorientationofaproteinwithrespecttothemembraneandcanbedetermined by the presence, or absence, and organization within the protein sequence of two features: endoplasmic reticulum signal peptides and alpha-helical transmembrane domains. These features allow protein sequences to be classified into one of five membrane organization categories: soluble intracellular proteins, soluble secreted proteins, type I membrane proteins, type II membrane proteins, and multi-spanning membrane proteins. Generation of protein isoformswithvariablemembraneorganizationscanchangeaprotein’ssubcellularlocalizationorassociationwiththe membrane. Application of MemO, a membrane organization annotation pipeline, to the FANTOM3 Isoform Protein Sequencemouseproteinsetrevealedthatwithinthe8,032transcriptionalunits(TUs)withmultipleproteinisoforms, 573hadvariationintheiruseofsignalpeptides,1,527hadvariationintheiruseoftransmembranedomains,and615 generatedproteinisoformsfromdistinctmembraneorganizationclasses.Themechanismsunderlyingthesetranscript variations were analyzed. While TUs were identified encoding all pairwise combinations of membrane organization categories,themost commonwas conversionofmembraneproteinsto solubleproteins.Observe