icd-II
Identifiers
Symbolicd-II
RfamRF04189
Other data
RNA typeCis-reg
GOGO:0010468
SOSO:0000370
PDB structuresPDBe

The icd-II non-coding RNA (ncRNA) is an RNA motif proposed as a Strong Riboswitch Candidate (SRC).[1] Icd-II 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).[2] Icd-II ncRNA has been located upstream of the icd gene, which codes for an NADP+-dependent isocitrate dehydrogenase (IDH) enzyme.[3] IDH is part of the citric acid cycle, and thus it participates in managing the carbon flux through this energy metabolism pathway. Icd-II ncRNA has been found in bacteria of the class beta proteobacteria, particularly in Polynucleobacter genus. Icd-II RNA secondary structure consists of a three-stem junction, where the ribosome binding site (RBS) of the adjacent open reading frame (ORF) is predicted to be involved in the first base-paired stem. It has been proposed that icd-II ncRNA can function as a riboswitch that regulates translation initiation of its associate ORF.

References

  1. ↑ 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.
  2. ↑ 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.
  3. ↑ Ishii, A.; Suzuki, M.; Sahara, T.; Takada, Y.; Sasaki, S.; Fukunaga, N. (November 1993). "Genes encoding two isocitrate dehydrogenase isozymes of a psychrophilic bacterium, Vibrio sp. strain ABE-1". Journal of Bacteriology. 175 (21): 6873–6880. doi:10.1128/jb.175.21.6873-6880.1993. ISSN 0021-9193. PMC 206812. PMID 8226630.


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