Washio T, Sasayama J, Tomita M
Laboratory for Bioinformatics, Graduate School of Media and Governance and Department of Environmental Information, Keio University, 5322 Endo, Fujisawa 252, Japan.
Nucleic Acids Res. 1998 Dec 1;26(23):5456-63. doi: 10.1093/nar/26.23.5456.
Free energy values of mRNA tertiary structures around stop codons were systematically calculated to surmise the hairpin-forming potential for all genes in each of the 16 complete prokaryote genomes. Instead of trying to detect each individual hairpin, we averaged the free energy values around the stop codons over the entire genome to predict how extensively the organism relies on hairpin formation in the process of transcription termination. The free energy values of Escherichia coli K-12 shows a sharp drop, as expected, at 30 bp downstream of the stop codon, presumably due to hairpin-forming sequences. Similar drops are observed for Haemophilus influenzae Rd, Bacillus subtilis and Chlamydia trachomatis, suggesting that these organisms also form hairpins at their transcription termination sites. On the other hand, 12 other prokaryotes- Mycoplasma genitalium, Mycoplasma pneumoniae, Synechocystis PCC6803, Helicobacter pylori, Borrelia burgdorferi, Methanococcus jannaschii, Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, Aquifex aeolicus, Pyrococcus horikoshii, Mycobacterium tuberculosis and Treponema pallidum -show no apparent decrease in free energy value at the corresponding regions. This result suggests that these prokaryotes, or at least some of them, may never form hairpins at their transcription termination sites.
系统地计算了终止密码子周围mRNA三级结构的自由能值，以推测16个完整原核生物基因组中每个基因形成发夹结构的潜力。我们没有试图检测每个单独的发夹结构，而是对整个基因组中终止密码子周围的自由能值进行平均，以预测生物体在转录终止过程中依赖发夹结构形成的程度。正如预期的那样，大肠杆菌K-12的自由能值在终止密码子下游30个碱基对处急剧下降，这可能是由于形成发夹结构的序列所致。在流感嗜血杆菌Rd、枯草芽孢杆菌和沙眼衣原体中也观察到类似的下降，这表明这些生物体在其转录终止位点也形成发夹结构。另一方面，其他12种原核生物——生殖支原体、肺炎支原体、集胞藻PCC6803、幽门螺杆菌、伯氏疏螺旋体、詹氏甲烷球菌、嗜热栖热放线菌、嗜热自养甲烷杆菌、嗜热栖热放线菌、火球菌、结核分枝杆菌和梅毒螺旋体——在相应区域的自由能值没有明显下降。这一结果表明，这些原核生物，或者至少其中一些，可能在其转录终止位点从不形成发夹结构。
