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

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.