Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species

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 Rhoindependent 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.

Phyletic distribution and conservation of the bacterial transcription termination factor Rho

“…Intrinsic transcription termination mechanisms could actually compensate for the absence of Rho. In agreement with this proposal, computational searches uncovered high frequencies of putative intrinsic terminator motifs in rho-less genomes of Firmicutes (de Hoon et al, 2005), Mollicutes (Kingsford et al, 2007) and Cyanobacteria (Vijayan et al, 2011). Notable exceptions are genomes of Mycoplasma genitalium, My.…”

“…Notable exceptions are genomes of Mycoplasma genitalium, My. pneumoniae and Synechocystis PCC 6803 in which putative intrinsic terminators were only scarcely detected (de Hoon et al, 2005;Kingsford et al, 2007;Washio et al, 1998). However, it remains currently uncertain if these exceptions are due to limitations of the computational search methods or if they reflect predominance of alternative, unidentified termination mechanisms (de Hoon et al, 2005;Kingsford et al, 2007).…”

Sequence-specific RNA binding mediated by the RNase PH domain of components of the exosome

“…Rho-independent terminators of prokaryotic genes usually contain a stem-loop structure followed by a stretch of uridylates (de Hoon et al 2005). The observation that at least one of the RNase PH domains of PNPase has affinity for U-rich stretches (i.e., the TNF-a ARE) may suggest a rationale for why the polymerase would choose to terminate these transcripts with a U-rich stretch.…”

Structure and evolution of gene regulatory networks in microbial genomes

“…However, unlike the case in E. coli, the Rho protein is dispensable in B. subtilis, suggesting a limited role for Rho-dependent termination in the latter. In fact, recent work demonstrated that more than 90% of the termination signals in B. subtilis and other Firmicutes are Rho-independent in nature [15]. Another group developed an efficient algorithm for rapid determination of Rho-independent terminators and demonstrated that outside the Firmicutes division, Rho-independent termination is also found to be dominant in the Neisseria, Vibrio and Pasteurellaceae genera [33].…”