page_title: Αr35 RNA
section_title: Promoter Analysis
hierarchical_section_title: Αr35 RNA / Promoter Analysis
caption_attribution_description: English: Graphic representation of the αr35 seed members' promoter region. All members presented putative σ70 promoters with -35 and -10 boxes marked in green and red respectively. The degenerated LysR recognition box is marked in blue.
context_page_description: αr35 is a family of bacterial small non-coding RNAs with representatives in a reduced group of α-proteobacteria from the order Rhizobiales. The first member of this family was found in a Sinorhizobium meliloti 1021 locus located in the symbiotic plasmid B. Further homology and structure conservation analysis have identified full-length SmrB35 homologs in other legume symbionts, as well as in the human and plant pathogens Ochrobactrum anthropi and Agrobacterium tumefaciens, respectively. αr35 RNA species are 139-142 nt long and share a common secondary structure consisting of two stem loops and a well conserved rho independent terminator. Most of the αr35 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions of the α-proteobacterial genomes.
context_section_description: All αr35 loci have recognizable σ⁷⁰-dependent promoters showing a -35/-10 consensus motif CTTAGAC-n17-CTATAT previously shown to be widely conserved among several other genera in the α-subgroup of proteobacteria. To identify binding sites for other known transcription factors we used the fasta sequences provided by RegPredict(http://regpredict.lbl.gov/regpredict/help.html), and used those position weight matrices (PSWM) provided by RegulonDB  (http://regulondb.ccg.unam.mx). We built PSWM for each transcription factor from the RegPredict sequences using the Consensus/Patser program, choosing the best final matrix for motif lengths between 14–30 bps if the corresponding length had not been previously specified (see "Consensus matrices" threshold (average E-value < 10E-10) for each matrix was established (see "Thresholded consensus" in http://gps-tools2.its.yale.edu). Moreover, we searched for conserved unknown motifs using MEME (http://meme.sdsc.edu/meme4_6_1/intro.html) and used relaxed regular expressions (i.e. pattern matching) over all Smr35B homologs promoters. Only an inverted repeat structure built around the motif T-N11-A was found 55 nt upstream of the transcription start site of SmrB35 in S. meliloti which is a degenerated motif of the known conserved nod boxes (Figure 4). This characteristic sequence has been proposed as the specific binding site for the LysR-type proteins. All promoter regions of the seed SmrB35 homologs presented the motif as well.
caption: Figure 4: Graphic representation of the αr35 seed members' promoter region. All members presented putative σ70 promoters with -35 and -10 boxes marked in green and red respectively. The degenerated LysR recognition box is marked in blue.
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