Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species

Open Access
Publisher Website
Google Scholar
Abstract
In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a transcriptional terminator. Some terminators rely on the presence of the Rho protein, whereas others function independently of Rho. Such Rho-independent terminators consist of an inverted repeat followed by a stretch of thymine residues, allowing us to predict their presence directly from the DNA sequence. Unlike in Escherichia coli, the Rho protein is dispensable in Bacillus subtilis, suggesting a limited role for Rho-dependent termination in this organism and possibly in other Firmicutes. We analyzed 463 experimentally known terminating sequences in B. subtilis and found a decision rule to distinguish Rho-independent transcriptional terminators from non-terminating sequences. The decision rule allowed us to find the boundaries of operons in B. subtilis with a sensitivity and specificity of about 94%. Using the same decision rule, we found an average sensitivity of 94% for 57 bacteria belonging to the Firmicutes phylum, and a considerably lower sensitivity for other bacteria. Our analysis shows that Rho-independent termination is dominant for Firmicutes in general, and that the properties of the transcriptional terminators are conserved. Terminator prediction can be used to reliably predict the operon structure in these organisms, even in the absence of experimentally known operons. Genome-wide predictions of Rho-independent terminators for the 57 Firmicutes are available in the Supporting Information section. In prokaryotes, genes belonging to the same operon are transcribed in a single mRNA molecule. Transcription starts as the RNA polymerase binds to the promoter and continues until it reaches a transcriptional terminator. To understand the gene regulatory network of transcription in bacteria, it is important as a first step to determine the operon structure. In this paper, the authors show that (unlike in Escherichia coli) most terminators in Bacillus subtilis function independently of the terminator protein Rho. As these Rho-independent terminators consist of an inverted repeat followed by a stretch of thymine residues, their presence can be predicted directly from the DNA sequence. The authors derived a decision rule by analyzing experimentally known terminating sequences in B. subtilis, and show that the operon boundaries can be found with a high accuracy (about 94%) in B. subtilis and other Firmicutes, even in the absence of experimentally known operons in the given organism. The properties of the transcriptional terminators are shown to be conserved within the Firmicutes phylum. For bacteria other than Firmicutes, the prediction accuracy is considerably lower, suggesting that Rho-dependent or possibly currently unknown termination mechanisms are important in these organisms.