内生菌KM-1-2全基因组ORFs信号肽和分泌蛋白预测及功能分析

Genome-wide prediction and analysis of the secretory proteins and ORFs signal peptide of ginkgo endophyte KM-1-2

摘要:

[目的]内生菌普遍存在于植物中，与宿主在长期的进化中形成了互利共生的关系。目前对内生菌和植物之间的互作机制研究较少，为深入了解银杏叶内生菌KM-1-2与寄主植物作用机制，本研究对其分泌蛋白进行预测，并明确其特征。[方法]组合使用信号肽分析软件SignalP，跨膜螺旋结构分析软件TMHMM 2.0和Phobius，蛋白质细胞定位软件PSORT，亚细胞定位软件TargetP和GPI锚定位点分析软件big-PI Predictor，预测KM-1-2基因组范围内所有分泌蛋白，定义为分泌组。[结果]KM-1-2全基因组5299条蛋白序列中发现271个具有典型信号肽的分泌蛋白，占全基因组的2.4%；编码这些蛋白的ORF最短为61 bp，最大为2105 bp，平均为373 bp；引导它们的信号肽长度分布在15-37 aa之间，平均为24 aa。信号肽中出现频率最高的氨基酸依次为丙氨酸、亮氨酸和缬氨酸，信号肽切割类型多属于A-X-A型，即SPI切割类型。共66个蛋白质有功能描述，其中包括26个酶类。这些酶主要包括各种糖苷水解酶、酯酶、蛋白酶、碳氧裂解酶等。[结论]通过上述生物信息学分析方法有效实现了银杏叶内生菌KM-1-2分泌蛋白的预测，这些分泌蛋白功能涉及较多的酶类以及其他未知功能，为进一步研究内生菌和植物的互作提供了基础。

Abstract:

[Objective] Endophytes are widespread in plants and build long-term mutually beneficial symbiotic relationship with the host. However, the mechanism of their interactions with the host needs further study. To explore the mechanism of endophytic bacterium ginkgo endophyte KM-1-2, we managed to forecast its secretory proteins based on its genome and explicit characteristics.[Methods] Signal peptide analysis software SignalP, transmembrane helical structure analysis software TMHMM and Phobius, cells position software PSORT, subcellar localization software TargetP and GPI anchor site analysis software big-PI Predictor were used to predict the scope of all secreted proteins, which were defined as secretome.[Results] Altogether 128 typical signal peptide secretory proteins were screened out of 5299 protein sequences in KM-1-2 genome, accounting for 2.4% of the whole genome. The shortest ORF encoding these proteins is 61 bp, the longest one is 2105 bp and the average is 373 bp. The length of the signal peptide guiding secretory protein was distributed between 15 to 37 aa, with the average length of 24 aa. Amino acid with the highest present frequency of signal peptide in proper order is alanine, leucine and valine. The type of signal peptide cleavage belongs to A-X-A which named SPI cleavage type. Among the total secretory proteins 66 pieces have functional description and 26 pieces were enzymes. These enzymes mainly include glycoside hydrolase, esterase transferase, REDOX enzyme and carbon oxygen lyase.[Conclusion] The predicted secretory proteins of Streptomyces lavendulae KM-1-2 were achieved through bioinformatics analysis. These secretory proteins involved some enzymes and other unknown functions. This result laid the foundation for further study between endophyte and host.