全基因组预测Phenylobacterium zucineum HLK1^T的外排蛋白

Genome-wide identification of exported proteins of the novel bacterium Phenylobacterium zucineum HLK1^T using a consensus computational strategy

目的:通过搜索Phenylobacterium zucineum HLK1T全基因组编码蛋白的N-端信号肽,跨膜α-螺旋等外排信号来预测其外排蛋白。方法:应用SingalPV3.0、LipoPV1.0、Phobius和TMHMM2.0对HLK1T基因组所编码的蛋白进行综合预测;对保守序列用手工方法进行搜索,预测型蛋白和TAT通路蛋白。对预测到的外排蛋白进行COG分类。结果:HLK1T基因组编码的3861个蛋白中有1378个(35.7%)为外排蛋白,其中以跨膜蛋白为最多,共预测到735个(占总蛋白的19.0%,外排蛋白的53.3%)。此外,它还编码499个型分泌蛋白(12.9%,36.2%)和101个脂蛋白(2.6%,7.3%),以及4个型蛋白和12个TAT通路蛋白。根据COG分类,这些外排蛋白中与无机离子转运和代谢相关的P蛋白以及功能未明的S蛋白为最多。结论:HLK1T编码大量外排蛋白,这些蛋白可能在细菌与宿主的相互作用以及胞内寄生的过程中发挥重要作用。

Objective： To predict the exported proteins of the novel bacterium Phenylobacterium zucineum HLK1^T using genome-wide computational identification by searching the export signals including N-terminal signal peptides and α-transmembrane helices. Methods： The computational identification of signal sequences was based on a consensus between multiple predictive tools, including SignalP V3.0,LipoP V1.0,Phobius and TMHMM 2.0. Type Ⅳ signal peptides and proteins exported via TAT machinery were searched manually based on the conservative motifs. All the predicted proteins were classified according to the Cluster of Orthologous Group （COG） standard. Results： In the total 3 861 proteins encoded by P. zucineum HLK1^T 1 378 （35.7%） were predicted to be exported proteins,most of which （totally 735,19.0% of the proteome and 53. 3% of all the exported proteins） were uncleavable transmembrane helices. In addition, 499 type I signal peptides （12.9%,36.2%）,101 lipoproteins （2.6%,7.3%） were also identified.Four Type Ⅳ signal peptides and 12 TAT proteins were detected as well. According to the COG classification standard,most of these exported proteins were P proteins related to inorganic ion transport and metabolism and S proteins whose functions were unknown. Conclusion. The genome of HLK1^T coded various types of exported proteins which may play an important role in the interaction between P. zucineum and the host cell,and facilitate the strain to invade into the cell.