Gao Xiang, Vander Velden Kent A, Voytas Daniel F, Gu Xun
Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa 50011, USA.
BMC Bioinformatics. 2005 Jun 1;6:137. doi: 10.1186/1471-2105-6-137.
Many protein families have undergone functional divergence after gene duplications such that current subgroups of the family carry out overlapping but distinct biological roles. For the protein families with known functional subtypes (a functional split), we developed the software, SplitTester, to identify potential regions that are responsible for the observed distinct functional subtypes within the same protein family.
Our software, SplitTester, takes a multiple protein sequences alignment as input, generated from protein members of two subgroups with known functional divergence. SplitTester was designed to construct the neighbor joining tree (a split cluster) from variable-sized sliding windows across the alignment in a process called split-clustering. SplitTester identifies the regions, whose split cluster is consistent with the functional split, but may be inconsistent with the phylogeny of the protein family. We hypothesize that at least some number of these identified regions, which are not following a random mutation process, are responsible for the observed functional split. To test our method, we used reverse transcriptase from a group of Pseudoviridae retrotransposons: to identify residues specific for diverged primer recognition. Candidate regions were then mapped onto the three dimensional structures of reverse transcriptase. The locations of these amino acids within the enzyme are consistent with their biological roles.
SplitTester aims to identify specific domain sequences responsible for functional divergence of subgroups within a protein family. From the analysis of retroelements reverse transcriptase family, we successfully identified the regions splitting this family according to the primer specificity, implying their functions in the specific primer selection.
许多蛋白质家族在基因复制后发生了功能分化，使得该家族当前的亚组执行重叠但不同的生物学功能。对于具有已知功能亚型（功能分化）的蛋白质家族，我们开发了SplitTester软件，以识别同一蛋白质家族中导致观察到的不同功能亚型的潜在区域。
我们的软件SplitTester以多个蛋白质序列比对作为输入，该比对由具有已知功能分化的两个亚组的蛋白质成员生成。SplitTester旨在通过一种称为分裂聚类的过程，从比对中的可变大小滑动窗口构建邻接树（分裂簇）。SplitTester识别出其分裂簇与功能分化一致，但可能与蛋白质家族系统发育不一致的区域。我们假设这些识别出的区域中至少有一些并非遵循随机突变过程，而是导致了观察到的功能分化。为了测试我们的方法，我们使用了一组假病毒科反转录转座子的逆转录酶：以识别对于分化的引物识别具有特异性的残基。然后将候选区域映射到逆转录酶的三维结构上。这些氨基酸在酶内的位置与其生物学功能一致。
SplitTester旨在识别蛋白质家族中亚组功能分化所涉及的特定结构域序列。通过对反转录元件逆转录酶家族的分析，我们成功地根据引物特异性识别出了该家族的分裂区域，这暗示了它们在特定引物选择中的功能。
