Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels.
Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels.
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DOI：
10.1186/1471-2105-14-229
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发表时间：
2013-07-18
影响因子：
3
通讯作者：
Pérez-Pulido AJ
中科院分区：
文献类型：
--
作者：
Parras-Moltó M;Campos-Laborie FJ;García-Diéguez J;Rodríguez-Griñolo MR;Pérez-Pulido AJ
大多数蛋白质是在特定的细胞区室中进化的，这限制了它们的功能和潜在的相互作用。另一方面，基序定义了蛋白质家族成员之间保守的氨基酸排列，并代表了为蛋白质序列分配功能的强大工具。理想的基序将识别蛋白质家族的所有成员，但实际上许多基序可识别家族成员和不相关的蛋白质，分别称为真阳性（TP）和假阳性（FP）序列。为了解决蛋白质基序、蛋白质功能和细胞定位之间的关系，我们系统地将亚细胞定位数据分配给综合 PROSITE 序列基序数据库中的基序序列。使用这些数据，我们分析了定位和功能之间的关系。我们发现 TP 和 FP 有很强的定位于不同区室的倾向。当考虑多个定位时，TP 通常分布在相关的细胞区室之间。我们还发现了 FP 集中在特定亚细胞区域的情况，表明与相同基序的 TP 序列可能存在功能或进化关系。我们的研究结果表明，亚细胞定位的系统检查有可能揭示包含基序的序列之间的进化和功能关系。我们相信这种类型的分析补充了现有的主题注释，并可以帮助解释它们。我们的结果揭示了细胞器的进化，并有可能为新的亚细胞定位和功能预测算法奠定基础。
Most proteins have evolved in specific cellular compartments that limit their functions and potential interactions. On the other hand, motifs define amino acid arrangements conserved between protein family members and represent powerful tools for assigning function to protein sequences. The ideal motif would identify all members of a protein family but in practice many motifs identify both family members and unrelated proteins, referred to as True Positive (TP) and False Positive (FP) sequences, respectively. To address the relationship between protein motifs, protein function and cellular localization, we systematically assigned subcellular localization data to motif sequences from the comprehensive PROSITE sequence motif database. Using this data we analyzed relationships between localization and function. We find that TPs and FPs have a strong tendency to localize in different compartments. When multiple localizations are considered, TPs are usually distributed between related cellular compartments. We also identified cases where FPs are concentrated in particular subcellular regions, indicating possible functional or evolutionary relationships with TP sequences of the same motif. Our findings suggest that the systematic examination of subcellular localization has the potential to uncover evolutionary and functional relationships between motif-containing sequences. We believe that this type of analysis complements existing motif annotations and could aid in their interpretation. Our results shed light on the evolution of cellular organelles and potentially establish the basis for new subcellular localization and function prediction algorithms.
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影响因子：
5.5
作者：
Gabaldon, Toni;Snel, Berend;van Zimmeren, Frank;Hemrika, Wieger;Tabak, Henk;Huynen, Martijn A.
通讯作者：
Huynen, Martijn A.
影响因子：
64.5
作者：
Hoepfner, D;Schildknegt, D;Tabak, HF
通讯作者：
Tabak, HF
影响因子：
7
作者：
Scott, MS;Thomas, DY;Hallett, MT
通讯作者：
Hallett, MT
影响因子：
10.5
作者：
Kumar, A;Agarwal, S;Snyder, M
通讯作者：
Snyder, M
影响因子：
7.4
作者：
Okamoto, T;Shimada, T;Minamikawa, T
通讯作者：
Minamikawa, T