Fold usage on genomes and protein fold evolution
Fold usage on genomes and protein fold evolution
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DOI：
10.1002/prot.20506
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发表时间：
2005-09-01
影响因子：
2.9
通讯作者：
Deane, CM
中科院分区：
文献类型：
--
作者：
Abeln, S;Deane, CM
我们回顾了完整基因组的折叠用法，以探索蛋白质结构的进化。基因组上褶皱存在或缺失的模式让我们了解了褶皱之间的关系，不同褶皱的年龄，以及我们是如何得到我们今天看到的褶皱的。我们研究了描述蛋白质折叠使用的不同度量之间的关系，例如每个基因组的折叠拷贝数，每个折叠的家族数以及折叠发生的基因组数。我们通过搜索来自所有三个生命王国的157个已完成的基因组序列的结构域，获得了这些折叠使用的度量。在我们对这些测量的比较中，我们发现细菌在其基因组上比古细菌具有相对更多的独特折叠。真核生物被发现在它们的基因组上有更多的折叠拷贝。如果我们把不同的折叠类别分开，α / β类别在大型基因组中具有相对较少的不同折叠，在细菌中具有更多的折叠副本，并且在所有三个领域同时发生更多的折叠。这些结果可能表明大多数α / β褶皱的形成要早于其他褶皱。对于每个基因组的折叠拷贝，我们观察到预期的幂律分布，并且我们发现每个折叠的家庭数量也有类似的分布。然而，折叠在基因组中的分布更为复杂，这在很大程度上取决于折叠的类别和王国。我们还表明，在折叠使用的三种措施之间没有明确的关系。在许多基因组上发生的折叠不一定在每个基因组上都有许多副本。同样，有很多副本的折叠不一定有很多家族，反之亦然。
We review fold usage on completed genomes to explore protein structure evolution. The patterns of presence or absence of folds on genomes gives us insights into the relationships between folds, the age of different folds and how we have arrived at the set of folds we see today. We examine the relationships between different measures which describe protein fold usage, such as the number of copies of a fold per genome, the number of families per fold, and the number of genomes a fold occurs on. We obtained these measures of fold usage by searching for the structural domains on 157 completed genome sequences from all three kingdoms of life. In our comparisons of these measures we found that bacteria have relatively more distinct folds on their genomes than archaea. Eukaryotes were found to have many more copies of a fold on their genomes. If we separate out the different fold classes, the alpha/beta class has relatively fewer distinct folds on large genomes, more copies of a fold on bacteria and more folds occurring in all three kingdoms simultaneously. These results possibly indicate that most alpha/beta folds originated earlier than other folds. The expected power law distribution is observed for copies of a fold per genome and we found a similar distribution for the number of families per fold. However, a more complicated distribution appears for fold occurrence across genomes, which strongly depends on fold class and kingdom. We also show that there is not a clear relationship between the three measures of fold usage.. A fold which occurs on many genomes does not necessarily have many copies on each genome. Similarly, folds with many copies do not necessarily have many families or vice versa.