title: Subcellular localization of mammalian type II membrane proteins.
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 of 26% of the defined dataset. All reported localization data are presented in the LOCATE database (http://www.locate.imb.uq.edu.au).
authors.affiliation: Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland 4072, Australia.
authors.forename: Rajith N
authors.initials: RN
authors.lastname: Aturaliya
authors.forename: J Lynn
authors.initials: JL
authors.lastname: Fink
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Davis
authors.forename: Melvena S
authors.initials: MS
authors.lastname: Teasdale
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Hanson
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Miranda
authors.forename: Alistair R R
authors.initials: AR
authors.lastname: Forrest
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
authors.forename: Harukazu
authors.initials: H
authors.lastname: Suzuki
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Kanamori
authors.forename: Chikatoshi
authors.initials: C
authors.lastname: Kai
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Rohan D
authors.initials: RD
authors.lastname: Teasdale
mesh_terms: D000818:Animals; D006367:HeLa Cells; D006801:Humans; D008565:Membrane Proteins / Q000378:metabolism*; D051379:Mice; D015388:Organelles / Q000378:metabolism*
chemical_list: D008565:Membrane Proteins