Identifying novel peroxisomal proteins
Identifying novel peroxisomal proteins
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DOI：
10.1002/prot.21420
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发表时间：
2007-11-15
影响因子：
2.9
通讯作者：
Boden, Mikael
中科院分区：
文献类型：
--
作者：
Hawkins, John;Mahony, Donna;Boden, Mikael
过氧化物酶体是负责一系列重要代谢过程的小亚细胞区室。预测过氧化物酶体蛋白输入的努力受到物种变异和稀疏序列数据集与实验证实的本地化的挑战。我们提出了一个预测过氧化物酶体进口的基础上存在的优势过氧化物酶体靶向信号1（PTS 1），一个看似保守，但高度非特异性的主题。信号似乎依赖于与前面的残基的微妙依赖性。我们评估预测精度对两个替代的预测服务，PEROXIP和PTS 1预测。我们测试的完整性预测的原核和真核蛋白质组缺乏过氧化物酶体的范围。类似地，我们测试已知与训练数据不重叠的过氧化物酶体蛋白的准确性。该模型将RIKEN IPS 7小鼠蛋白质数据集中的许多蛋白质鉴定为潜在的新型过氧化物酶体蛋白质。其中三个在体外通过瞬时转染BHK-21细胞（Dhrs 2、Serhl和Ehhadh）中myc表位标记蛋白的免疫荧光检测得到证实。最终模型对两种替代方案具有上级特异性，准确性优于PEROXIP，与PTs 1预测剂相当。因此，我们提出的模型应该证明是非常宝贵的标记PTS 1靶向蛋白质的高置信度。我们使用预测筛选几个额外的真核基因组，以修改先前估计的过氧化物酶体蛋白的数量。可在http://pprowler.itee.uq.edu.au上获得。(C)2007 Wiley-Liss，Inc.
Peroxisomes are small subcellular compartments responsible for a range of essential metabolic processes. Efforts in predicting peroxisomal protein import are challenged by species variation and sparse sequence data sets with experimentally confirmed localization. We present a predictor of peroxisomal import based on the presence of the dominant peroxisomal targeting signal one (PTS1), a seemingly well conserved but highly unspecific motif. The signal appears to rely on subtle dependencies with the preceding residues. We evaluate prediction accuracies against two alternative predictor services, PEROXIP and the PTS1 PREDICTOR. We test the integrity of prediction on a range of prokaryotic and eukaryotic proteomes lacking peroxisomes. Similarly we test the accuracy on peroxisomal proteins known to not overlap with training data. The model identified a number of proteins within the RIKEN IPS7 mouse protein dataset as potentially novel peroxisomal proteins. Three were confirmed in vitro using immunofluorescent detection of myc-epitope-tagged proteins in transiently transfected BHK-21 cells (Dhrs2, Serhl, and Ehhadh).The final model has a superior specificity to both alternatives, and an accuracy better than PEROXIP and on par with PTs1 PREDICTOR. Thus, the model we present should prove invaluable for labeling PTS1 targeted proteins with high confidence. We use the predictor to screen several additional eukaryotic genomes to revise previously estimated numbers of peroxisomal proteins. Available at http://pprowler.itee.uq.edu.au. (C) 2007 Wiley-Liss, Inc.