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CarA ncRNA motif

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carA
Consensus secondary structure and sequence conservation of carA ncRNA motif
Identifiers
SymbolcarA
RfamRF04192
Other data
RNA typeCis-reg
GOGO:0010468
SOSO:0000370
PDB structuresPDBe

The carA non-coding RNA (ncRNA) is an RNA motif proposed as a Strong Riboswitch Candidate (SRC). CarA ncRNA has been recognized by a comparative sequence analysis in GC-rich intergenic regions (IGR) of bacteria, using a pipeline call Discovery of Intergenic Motifs PipeLine (DIMPL). CarA ncRNA was located upstream of carA gene which codes for the small subunit of carbamoyl phosphate synthase, which is an enzyme that catalyzes the first committed step in pyrimidine and arginine biosynthesis. CarA ncRNA has been found in bacteria of the class beta proteobacteria, particularly in Polynucleobacter genus. Its proposed secondary structure consists of an extended imperfect hairpin that is immediately upstream of the predicted ribosome binding site (RBS) of the adjacent open reading frame (ORF) suggesting a possible cis-regulatory function where ligand binding regulates translation initiation. CarA ncRNA motif, was reported twice, carA was recognised in Polynucleobacter necessarius genome, and carA-2 in a genome of Beta proteobacterium CB.

References

  1. Brewer, Kenneth I.; Gaffield, Glenn J.; Puri, Malavika; Breaker, Ronald R. (2021-09-15). "DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria". Bioinformatics. 38 (2): 533–535. doi:10.1093/bioinformatics/btab624. ISSN 1367-4811. PMC 8723152. PMID 34524415.
  2. "Biosynthesis and metabolism of arginine in bacteria". Microbiological Reviews. 51 (1): 178. March 1987. doi:10.1128/mr.51.1.178-178b.1987. ISSN 0146-0749. PMC 373097. PMID 16350242.
  3. Brewer, Kenneth I.; Greenlee, Etienne B.; Higgs, Gadareth; Yu, Diane; Mirihana Arachchilage, Gayan; Chen, Xi; King, Nicholas; White, Neil; Breaker, Ronald R. (2021-05-10). "Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes". RNA Biology. 18 (12): 2417–2432. doi:10.1080/15476286.2021.1917891. ISSN 1555-8584. PMC 8632094. PMID 33970790.

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