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KMID : 1023520040270010095
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Korean Journal of Veterinary Service
2004 Volume.27 No. 1 p.95 ~ p.101
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Analysis of putative promoter sites in Babesia bovis rap-l and B equi ema-l intergenic nucleotides
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Kwak Dong-Mi
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Abstract
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Babesia bovis rap-1 and B equi ema-1 intergenic(IG) nucleotides were analyzed and compared for identifying putative promoter sites using computer programs. The reason to initiate this research was to determine if IG nucleotides of Babesia genes that are predicted to be involved in erythrocyte invasion have functions regulating gene transcription and translation, which can be applied to functional gene knockout. Four IG sequences used included BbIG5(B bovis rap-1 5’ IG), BblG3(B bovis rap-1 3’ IG), BeIG5(B equi ema-1 5’ IG) and BeIG3(B equi ema-1 3’ IG). BbIG5 contained a putative promoter at nucleotide 197-246 with a predicted TATA-box and a transcription start site. BbIG3 had a putative promoter at nucleotide 270-320 with two predicted TATA-boxes and a transcription start site. BeIG3 had a putative promoter at nucleotide 155-205 with a predicted TATA-box and a transcription start site. Putative promoter sites in these three sequences mentioned above were identified with score cutoff 0.8, which means detection of about 40% recognized promoters with 0.1-0.4% false positives. In contrast, BeIG5 had a putative promoter at nucleotide 163-213 with score cutoff 0.8, but neither TATA-box nor transcription start site were recognized. However, BeIG5 had a putative promoter at nucleotide 388-438 with a predicted TATA-box and a transcription start site when score cutoff was decreased to 0.18, which means detection of about 70% recognized promoters with 2.2-5.3% false positives. These sequences with putative promoters can be tested if they have functions regulating gene transcription and translation.
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KEYWORD
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Babesia spp, Intergenic nucleotide, Putative promoter, TATA-box
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