Identification and characterization of novel small RNAs in the aspS–yrvM intergenic region of the Bacillus subtilis genome

Abstract

A novel RNA species was isolated from Bacillus subtilis, and its sequence was determined and mapped to its genetic position. This RNA was termed BS190 RNA from the length of its mature form (190 nt), and the gene encoding it is located within the aspS-yrvM intergenic region of the B. subtilis genome. Northern blotting revealed that the novel RNA species is transcribed in vegetative cells as a larger precursor (BS201 RNA, 201 nt). After transcription, the 5' end of the precursor is processed to generate the mature form, BS190 RNA. A computer-aided prediction of the secondary structure of BS190 RNA showed that it can be folded into a single hairpin structure with some bulge structures. The authors found that the growth rate of a ∆BS190 mutant strain of B. subtilis was reduced when compared to the wild-type. A phylogenetic comparison of the sequence of the BS190 RNA gene with sequences from the databases suggests that RNA related to BS190 RNA appears to be encoded in the genomes of Bacillus halodurans and Listeria monocytogenes.

In vivo and in vitro analysis of 6S RNA-templated short transcripts inBacillus subtilis

“…1E] indicated that the 5'-extended version is the primary transcript carrying a 5'-triphosphate protecting the RNA from 5'-exonucleolytic degradation. These findings are consistent with 6S-1 RNA being transcribed as a 201 nt long 5'-precursor that is processed to its mature form (190 nt), 16 in line with the appearance of two bands in the northern blot (Fig. 1B).…”

“…1B), in line with previous observations. 6,15 As reported before, 6,16 6S-1 RNA occurs as a 201-nt precursor form (p6S-1) and a 190-nt mature RNA (m6S-1) in B. subtilis cells (Fig. 1B).…”

“…S1), thus confirming the maturation site at position 11 of p6S-1, consistent with results from primer extension analysis. 16 cDNA library construction and 6S RNA reads. We have addressed the question whether B. subtilis 6S-1 and 6S-2 RNAs serve as templates for the synthesis of short pRNA transcripts, which have previously been identified in E. coli and Helicobacter pylori, 12,13,17 and more recently also in B. subtilis, but with low read coverage (ref.…”

“…and Roland K. hartmann 1, encodes at least two 6S RNA homologs, termed 6S-1 (bsrA) and 6S-2 (bsrB). 15,16 Both RNAs were co-immunoprecipitated with the σ A housekeeping RNAP holoenzyme using antibodies against σ A or the α-subunit. 7 So far, it has been unclear whether these 6S RNAs have functions identical or similar to that of E. coli 6S RNA.…”

Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs—commonalities and differences

“…At their discovery, the genes for the two ncRNAs were termed bsrA and bsrB Suzuma et al 2002), but their nature as 6S RNAs was only unveiled in a later study by the Wassarman group (Trotochaud and Wassarman 2005). Both RNAs were shown to coimmunoprecipitate with the σ A housekeeping RNAP holoenzyme using antibodies against σ A or the core subunit α (Trotochaud and Wassarman 2005).…”