The YkkC/YxkD leader is a conserved

Conserved sequence

In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...

 RNA structure

Cis-regulatory element

A cis-regulatory element or cis-element is a region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA . This term is constructed from the Latin word cis, which means "on the same side as". These cis-regulatory elements are often binding sites for one or...

 found upstream of the ykkC and yxkD genes in Bacillus subtilis

Bacillus subtilis

Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...

and related genes in other bacteria. The function of this family is unclear although it has been suggested that it may function to switch on efflux pumps and detoxification systems in response to harmful environmental molecules. The Thermoanaerobacter tengcongensis sequence AE013027 overlaps with that of purine riboswitch

Purine riboswitch

Purine riboswitches are RNA structures that regulate protein biosynthesis in response to purines. In general, riboswitches are metabolite-binding domains within certain messenger RNAs that act as precision sensors for their corresponding targets...

 suggesting that the two riboswitch

Riboswitch

In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the...

es may work in conjunction to regulate the upstream gene which codes for TTE0584 (Q8RC62), a member of the permease

Permease

The permeases are membrane transport proteins, a class of multipass transmembrane proteins that facilitate the diffusion of a specific molecule in or out of the cell by passive transport...

 family.

The mini-ykkC RNA motif

Mini-ykkC RNA motif

The mini-ykkC RNA motif is a putative RNA structure that is conserved in bacteria. The motif consists of two conserved stem-loops whose terminal loops contain the RNA sequence ACGR, where R represents either A or G. Mini-ykkC RNAs are widespread in Proteobacteria, but some are predicted in other...

 is a putative cis-regulatory element that apparently regulates similar gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

s to those regulated by the ykkC/yxkD leader; therefore, these RNA motifs might have similar functions. However, the mini-ykkC RNA motif is simpler in structure and has fewer highly conserved nucleotide

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

positions than the ykkC-yxkD leader.

The ykkC-III RNA motif is a distinct candidate cis-regulatory RNA that appears to regulate genes related to the preceding motifs. Although the structure of ykkC-III RNAs does not resemble ykkC/yxkD RNAs, both have a structure complexity that led to the proposal that they represent riboswitches, unlike mini-ykkC RNAs. The ykkC-III motif has a rigidly conserved ACGA sequence within it that resembles a less rigidly conserved ACGA or ACGG sequence found in mini-ykkC RNAs, but it is unknown whether this observation relates to a biological relationship.