Beeby Morgan, Bobik Thomas A, Yeates Todd O
UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California 90095, USA.
Protein Sci. 2009 Jan;18(1):69-79. doi: 10.1002/pro.1.
Bacterial microcompartments are supramolecular protein assemblies that function as bacterial organelles by compartmentalizing particular enzymes and metabolic intermediates. The outer shells of these microcompartments are assembled from multiple paralogous structural proteins. Because the paralogs are required to assemble together, their genes are often transcribed together from the same operon, giving rise to a distinctive genomic pattern: multiple, typically small, paralogous proteins encoded in close proximity on the bacterial chromosome. To investigate the generality of this pattern in supramolecular assemblies, we employed a comparative genomics approach to search for protein families that show the same kind of genomic pattern as that exhibited by bacterial microcompartments. The results indicate that a variety of large supramolecular assemblies fit the pattern, including bacterial gas vesicles, bacterial pili, and small heat-shock protein complexes. The search also retrieved several widely distributed protein families of presently unknown function. The proteins from one of these families were characterized experimentally and found to show a behavior indicative of supramolecular assembly. We conclude that cotranscribed paralogs are a common feature of diverse supramolecular assemblies, and a useful genomic signature for discovering new kinds of large protein assemblies from genomic data.
细菌微区室是超分子蛋白质组装体，通过将特定酶和代谢中间体分隔开来发挥细菌细胞器的功能。这些微区室的外壳由多种旁系同源结构蛋白组装而成。由于旁系同源蛋白需要共同组装，它们的基因通常从同一个操纵子一起转录，从而产生一种独特的基因组模式：多个通常较小的旁系同源蛋白在细菌染色体上紧密相邻编码。为了研究这种模式在超分子组装体中的普遍性，我们采用了比较基因组学方法来寻找与细菌微区室呈现相同基因组模式的蛋白质家族。结果表明，多种大型超分子组装体符合这种模式，包括细菌气荚膜、细菌菌毛和小分子热休克蛋白复合物。该搜索还检索到了几个目前功能未知但分布广泛的蛋白质家族。对其中一个家族的蛋白质进行了实验表征，发现其表现出超分子组装的行为。我们得出结论，共转录旁系同源蛋白是多种超分子组装体的共同特征，也是从基因组数据中发现新型大型蛋白质组装体的有用基因组特征。
