Prediction of transcriptional terminators in bacillus subtiiis and species

Abstract

n prokaryoies, genes beiorsging to the same operon are transcribed in a single srsR-4A molecule. Transcription starts as the RNA poSymerase binds to the promoter and continues ursti it reaches a transcdptionai termirsator. Some terminators reay ors the presence of the Rho protein, whereas others function Sndependentiy of Rho. Such Rhoirsdepersdeint terminators consist of art inverted repeat foEiowed by a stretch of thymine residues, avowing us to predict their presence directiy from the D?JA sequence. Unaike in Escherkhitz col, the Rho proteirs is dispertsabie in Bacillus subtilis, suggesting a ilmited roie for Rho-dependent termisiatiors 'm this organism arse possibiy irs other Firmkutes. We asiaSysed 463 experimerstaiay krsowrs terminatirsg seqwesices irs S, sabtHis arsd found a decision rwie to distirsgwish Rho-irsdepersdent transcriptiona terminators from nou-terminatang sequences. The decision risie aiaowed us to find the boundaries of operorss ir 8, subtiiis with a sensitivity and specificity of about 94%. Usirsg the same decision ruie, we foynd art average sensitivity of 94% for S? bacteria belonging te the Finrikutes phyksm, artd a considerably iower sensitivity for other bacteria. Our anaiysis shows that Rho-independersi iermirsation is dominant for Firmkutes irs general, and that the properties of the transcriptionaS terminators are conserved. Termisiator predictsosi cars be used to refiabiy predict the operon structure irs these organisms, even in the absence of experimerstauy known operorss. Genome-wide predictions of Rho-irsdepersderst termisiators for the 57 Fsmkutes are avaiiabfe irs the Ssjpportisig information section. Copyright: £> 2005 De Hoon et al. '.