Differential-display reverse transcription-PCR (DDRT-PCR): a new technology for molecular detection and studying one of the antagonistic factors of Bacillus endophyticus strain SA against Staphylococcus aureus (MRSA)

Differential Display (DDRT-PCR) is a powerful technique for analyzing differences in gene expression. In-vivo expression technologies and differential display RT-PCR are providing new approaches to further examine a microbe’s response to experimental conditions which more closely resemble natural microbial associations and habitats. In this study, Bacillus endophyticus strain SA isolated from the inner tissue of the stem of the cultivated plant (Salvadora persica, Asir, Kingdom of Saudi Arabia) produces an antagonistic factor. This factor has a broad spectrum of activity against Gram-positive and specifically against Staphylococcus aureus (MRSA). The antagonistic factor was isolated from the bacterial culture medium and purified by thin layer chromatography technique, then analyzed by GC–MS analysis. Identification of the producer strain was performed using the partial nucleotide sequence of 16S rRNA gene, which indicated that this strain is identical to B. endophyticus with 99 % similarity. The sequence of this strain was deposited at NCBI GenBank under accession number KF011545. Application of differential display RT-PCR revealed that the isolate was able to up-regulate a gene with serine protease like protein. The protein is well known as antimicrobial agent and was reported to be produced by plants, animals and insects. Serine protease is also known to be produced by bacteria for purposes oth er than bacterial–bacterial antagonistic effect, which has been confirmed by this study.