Analysis of complete genomes suggests that many prokaryotes do not rely onhairpin formation in transcription termination

Free energy values of mRNA tertiary structures around stop codons were syst ematically calculated to surmise the hairpin-forming potential for all gene s in each of the 16 complete prokaryote genomes. Instead of trying to detec t each individual hairpin, we averaged the free energy values around the st op codons over the entire genome to predict how extensively the organism re lies 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, Bacill us 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, Synecho cystis PCC6803, Helicobacter pylori, Borrelia burgdorferi, Methanococcus ja nnaschii, Archaeoglobus fulgidus, Methanobacterium thermo-autotrophicum, Aq uitex aeolicus, Pyrococcus horikoshii, Mycobacterium tuberculosis and Trepo nema pallidum-show no apparent decrease in free energy value at the corresp onding regions. This result suggests that these prokaryotes, or at least so me of them, may never form hairpins at their transcription termination site s.