School of Life Sciences and the State Key Lab of Agrobiotechnology, the Chinese University of Hong Kong, Shatin, NT, Hong Kong.
PLoS One. 2013 Apr 4;8(4):e59754. doi: 10.1371/journal.pone.0059754. Print 2013.
Type III secretion system (T3SS) plays important roles in bacteria and host cell interactions by specifically translocating type III effectors into the cytoplasm of the host cells. The N-terminal amino acid sequences of the bacterial type III effectors determine their specific secretion via type III secretion conduits. It is still unclear as to how the N-terminal sequences guide this specificity. In this work, the amino acid composition, secondary structure, and solvent accessibility in the N-termini of type III and non-type III secreted proteins were compared and contrasted. A high-efficacy mathematical model based on these joint features was developed to distinguish the type III proteins from the non-type III ones. The results indicate that secondary structure and solvent accessibility may make important contribution to the specific recognition of type III secretion signals. Analysis also showed that the joint feature of the N-terminal 6(th)-10(th) amino acids are especially important for guiding specific type III secretion. Furthermore, a genome-wide screening was performed to predict Salmonella type III secreted proteins, and 8 new candidates were experimentally validated. Interestingly, type III secretion signals were also predicted in gram-positive bacteria and yeasts. Experimental validation showed that two candidates from yeast can indeed be secreted through Salmonella type III secretion conduit. This research provides the first line of direct evidence that secondary structure and solvent accessibility contain important features for guiding specific type III secretion. The new software based on these joint features ensures a high accuracy (general cross-validation sensitivity of ∼96% at a specificity of ∼98%) in silico identification of new type III secreted proteins, which may facilitate our understanding about the specificity of type III secretion and the evolution of type III secreted proteins.
III 型分泌系统 (T3SS) 通过将 III 型效应物特异性地转运到宿主细胞的细胞质中，在细菌和宿主细胞相互作用中发挥重要作用。细菌 III 型效应物的 N 端氨基酸序列决定了它们通过 III 型分泌管的特异性分泌。目前尚不清楚 N 端序列如何指导这种特异性。在这项工作中，比较和对比了 III 型和非 III 型分泌蛋白的 N 端的氨基酸组成、二级结构和溶剂可及性。基于这些联合特征开发了一种高效的数学模型，用于将 III 型蛋白与非 III 型蛋白区分开来。结果表明，二级结构和溶剂可及性可能对 III 型分泌信号的特异性识别做出重要贡献。分析还表明，N 端第 6-10 个氨基酸的联合特征对于指导特定的 III 型分泌尤为重要。此外，还进行了全基因组筛选以预测沙门氏菌 III 型分泌蛋白，并通过实验验证了 8 个新的候选蛋白。有趣的是，革兰氏阳性菌和酵母中也预测到了 III 型分泌信号。实验验证表明，酵母中的两个候选蛋白确实可以通过沙门氏菌 III 型分泌管分泌。这项研究提供了直接证据，表明二级结构和溶剂可及性包含指导特定 III 型分泌的重要特征。基于这些联合特征的新软件确保了新的 III 型分泌蛋白的计算识别具有较高的准确性（特异性为 98%时，通用交叉验证敏感性约为 96%），这可能有助于我们理解 III 型分泌的特异性和 III 型分泌蛋白的进化。
