AIST, Computational Biology Research Center, Tokyo, Aomi 135-0064, Japan.
BMC Genomics. 2011 Jan 28;12:79. doi: 10.1186/1471-2164-12-79.
The outer membranes of mitochondria are thought to be homologous to the outer membranes of Gram negative bacteria, which contain 100's of distinct families of β-barrel membrane proteins (BOMPs) often forming channels for transport of nutrients or drugs. However, only four families of mitochondrial BOMPs (MBOMPs) have been confirmed to date. Although estimates as high as 100 have been made in the past, the number of yet undiscovered MBOMPs is an open question. Fortunately, the recent discovery of a membrane integration signal (the β-signal) for MBOMPs gave us an opportunity to look for undiscovered MBOMPs.
We present the results of a comprehensive survey of eukaryotic protein sequences intended to identify new MBOMPs. Our search employs recent results on β-signals as well as structural information and a novel BOMP predictor trained on both bacterial and mitochondrial BOMPs. Our principal finding is circumstantial evidence suggesting that few MBOMPs remain to be discovered, if one assumes that, like known MBOMPs, novel MBOMPs will be monomeric and β-signal dependent. In addition to this, our analysis of MBOMP homologs reveals some exceptions to the current model of the β-signal, but confirms its consistent presence in the C-terminal region of MBOMP proteins. We also report a β-signal independent search for MBOMPs against the yeast and Arabidopsis proteomes. We find no good candidates MBOMPs in yeast but the Arabidopsis results are less conclusive.
Our results suggest there are no remaining MBOMPs left to discover in yeast; and if one assumes all MBOMPs are β-signal dependent, few MBOMP families remain undiscovered in any sequenced organism.
人们认为线粒体的外膜与革兰氏阴性细菌的外膜同源，革兰氏阴性细菌的外膜含有 100 多种不同的β桶膜蛋白（BOMP）家族，这些家族通常形成营养物质或药物运输的通道。然而，迄今为止只确认了四种线粒体 BOMP 家族（MBOMP）。尽管过去的估计高达 100 种，但尚未发现的 MBOMP 数量仍是一个悬而未决的问题。幸运的是，最近发现了一种用于 MBOMP 的膜整合信号（β-信号），这为我们寻找未发现的 MBOMP 提供了机会。
我们介绍了一项针对真核生物蛋白质序列的全面调查结果，旨在识别新的 MBOMP。我们的搜索利用了最近关于β-信号的结果，以及结构信息和一种基于细菌和线粒体 BOMP 训练的新型 BOMP 预测器。我们的主要发现是，如果假定像已知的 MBOMP 一样，新的 MBOMP 将是单体和β-信号依赖的，那么几乎没有 MBOMP 有待发现，这只是一个间接证据。除此之外，我们对 MBOMP 同源物的分析揭示了当前β-信号模型的一些例外情况，但证实了它在 MBOMP 蛋白的 C 末端区域的一致存在。我们还报告了针对酵母和拟南芥蛋白质组的β-信号独立的 MBOMP 搜索。我们在酵母中没有发现好的 MBOMP 候选物，但拟南芥的结果不太确定。
我们的结果表明，在酵母中没有剩余的 MBOMP 有待发现；并且如果假定所有 MBOMP 都依赖β-信号，那么在任何测序生物中都很少有未发现的 MBOMP 家族。
