Subcellular localization of mammalian type II membrane proteins

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R N AturaliyaR D Teasdale

Abstract

Application of a computational membrane organization prediction pipeline, MemO, identified putative type II membrane proteins as proteins predicted to encode a single alpha-helical transmembrane domain (TMD) and no signal peptides. MemO was applied to RIKEN's mouse isoform protein set to identify 1436 non-overlapping genomic regions or transcriptional units (TUs), which encode exclusively type II membrane proteins. Proteins with overlapping predicted InterPro and TMDs were reviewed to discard false positive predictions resulting in a dataset comprised of 1831 transcripts in 1408 TUs. This dataset was used to develop a systematic protocol to document subcellular localization of type II membrane proteins. This approach combines mining of published literature to identify subcellular localization data and a high-throughput, polymerase chain reaction (PCR)-based approach to experimentally characterize subcellular localization. These approaches have provided localization data for 244 and 169 proteins. Type II membrane proteins are localized to all major organelle compartments; however, some biases were observed towards the early secretory pathway and punctate structures. Collectively, this study reports the subcellular localization o...Continue Reading

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Citations

Jun 20, 2008·Bioinformatics·A D J van DijkR C H J van Ham
Nov 8, 2007·Nucleic Acids Research·Josefine SprengerRohan D Teasdale
Jan 24, 2008·Genome Biology·J Lynn FinkRohan D Teasdale
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Jan 1, 2012·Cells·Rajith N AturaliyaRohan D Teasdale
Mar 24, 2007·Molecular Medicine·Fabio MalavasiAlberto L Horenstein

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