HopC RNA motif
HopC RNA motif is a predicted cis-regulatory RNA element found in certain Helicobacter bacteria. It was discovered by comparing RNA sequences across related organisms and identifying a conserved RNA structure in the 5’ untranslated region (5’ UTR) of the hopCB operon, which contains the hopC and hopB genes.
In these bacteria, the hopCB operon is more active at low pH, and the HopCB proteins are believed to help the bacteria interact with human epithelial cells during stomach infection. The HopC RNA motif’s location in the 5’ UTR supports a role in regulating the expression of the hopCB operon, likely by affecting transcription or translation.
HopC RNAs are found exclusively in Helicobacter species, suggesting a specialized regulatory mechanism for this genus. The motif is cataloged in the Rfam database as RF01741, and a consensus secondary structure for hopC RNAs has been published.
Earlier ideas proposed a 13-nucleotide thymidine repeat upstream of hopCB as a regulator, but this sequence lies before the hopCB transcription start site and appears to be separate from the HopC RNA motif’s regulatory function.
Key references include Weinberg et al. (2010), which reported many candidate structured RNAs in bacteria and archaea; McGowan et al. (2003), who studied promoter activity in Helicobacter pylori; and Odenbreit et al. (2002), who explored factors involved in Helicobacter pylori adhesion.
This page was last edited on 1 February 2026, at 21:42 (CET).