Collection of regulogs for ykkC-yxkD (RF00442) RNA regulatory element
The ykkC-yxkD RNA motif is a conserved regulatory element found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The ykkCD operon encodes a multidrug resistance efflux pump with a broad specificity, whereas the yxkD gene function is unknown. Genetic reporter assays suggeste the ykkC RNA motif functions as a gene control element . Testing of a large collection of metabolites for binding to a ykkC RNA representative from B. subtilis (including putrescine, agmatine, spermidine, uric acid etc.) did not reveal a molecular effector of the ykkC regulatory RNA .
Additional conserved RNA structures, including mini-ykkC, have been identified associated with many of the same genes as the ykkC RNA. The mini-ykkC RNA motif is structurally distinct from the ykkC RNA. Nevertheless, both mini-ykkC and ykkC RNA motifs were hypothesized to respond to the same biological condition or effectors.
|Phylum||Regulog||RNA regulons (studied genomes)||RNA sites|
|Actinobacteria||ykkC-yxkD - Mycobacteriaceae||3 (9)||3|
|Cyanobacteria||ykkC-yxkD - Cyanobacteria||5 (14)||6|
|Firmicutes||ykkC-yxkD - Bacillales||8 (11)||11|
|Firmicutes||ykkC-yxkD - Clostridiaceae||9 (20)||11|
|Firmicutes||ykkC-yxkD - Lactobacillaceae||2 (15)||2|
|Firmicutes||ykkC-yxkD - Staphylococcaceae||1 (7)||1|
|Proteobacteria||ykkC-yxkD - Burkholderia||3 (8)||5|
|Proteobacteria||ykkC-yxkD - Enterobacteriales||1 (12)||1|
|Proteobacteria||ykkC-yxkD - Pseudomonadaceae||3 (8)||6|
|Proteobacteria||ykkC-yxkD - Ralstonia||1 (6)||2|
|Proteobacteria||ykkC-yxkD - Rhizobiales||7 (15)||7|
|Proteobacteria||ykkC-yxkD - Rhodobacterales||3 (15)||3|