The Bacillaceae-1 RNA motif comprises two distinct classes
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The Bacillaceae-1 RNA motif comprises two distinct classes. / González-Tortuero, Enrique; Anthon, Christian; Havgaard, Jakob H.; Geissler, Adrian S.; Breüner, Anne; Hjort, Carsten; Gorodkin, Jan; Seemann, Stefan E.
In: Gene, Vol. 841, 146756, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - The Bacillaceae-1 RNA motif comprises two distinct classes
AU - González-Tortuero, Enrique
AU - Anthon, Christian
AU - Havgaard, Jakob H.
AU - Geissler, Adrian S.
AU - Breüner, Anne
AU - Hjort, Carsten
AU - Gorodkin, Jan
AU - Seemann, Stefan E.
N1 - Publisher Copyright: © 2022 The Author(s)
PY - 2022
Y1 - 2022
N2 - Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis, we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches.
AB - Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis, we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches.
KW - 16S rRNA
KW - Bacillus subtilis
KW - Rfam
KW - Ribosomal RNA
KW - RNA secondary structure
KW - Structural switch
U2 - 10.1016/j.gene.2022.146756
DO - 10.1016/j.gene.2022.146756
M3 - Journal article
C2 - 35905857
AN - SCOPUS:85135768344
VL - 841
JO - Gene
JF - Gene
SN - 0378-1119
M1 - 146756
ER -
ID: 319163705