Aturaliya Rajith N, Fink J Lynn, Davis Melissa J, Teasdale Melvena S, Hanson Kelly A, Miranda Kevin C, Forrest Alistair R R, Grimmond Sean M, Suzuki Harukazu, Kanamori Mutsumi, Kai Chikatoshi, Kawai Jun, Carninci Piero, Hayashizaki Yoshihide, Teasdale Rohan D
Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland 4072, Australia.
Traffic. 2006 May;7(5):613-25. doi: 10.1111/j.1600-0854.2006.00407.x.
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).
应用一种计算性膜组织预测流程MemO，将推定的II型膜蛋白鉴定为预测编码单个α螺旋跨膜结构域（TMD）且无信号肽的蛋白质。将MemO应用于日本理化学研究所的小鼠同工型蛋白质组，以鉴定1436个非重叠基因组区域或转录单元（TU），这些区域仅编码II型膜蛋白。对具有重叠预测的InterPro和TMD的蛋白质进行审查，以排除假阳性预测，从而得到一个由1408个TU中的1831个转录本组成的数据集。该数据集用于制定一个系统方案，以记录II型膜蛋白的亚细胞定位。这种方法结合了挖掘已发表文献以识别亚细胞定位数据，以及基于高通量聚合酶链反应（PCR）的方法来实验性地表征亚细胞定位。这些方法已为244种和169种蛋白质提供了定位数据。II型膜蛋白定位于所有主要细胞器区室；然而，观察到对早期分泌途径和点状结构存在一些偏向性。总体而言，本研究报告了定义数据集中26%的亚细胞定位。所有报告的定位数据都呈现在LOCATE数据库（http://www.locate.imb.uq.edu.au）中。
