The ykkC/yxkD leader is a conserved

RNA structure Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quater ...

found

upstream Upstream may refer to: * Upstream (bioprocess) * ''Upstream'' (film), a 1927 film by John Ford * Upstream (networking) * ''Upstream'' (newspaper), a newspaper covering the oil and gas industry * Upstream (petroleum industry) * Upstream (software ...

of the ykkC and yxkD genes in ''

Bacillus subtilis ''Bacillus subtilis'', known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants, humans and marine sponges. As a member of the genus '' Baci ...

'' and related genes in other bacteria. The function of this family is unclear for many years although it has been suggested that it may function to switch on

efflux pump In microbiology, efflux is the moving of a variety of different compounds out of cells, such as antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals, bacterial metabolites and neurotransmitters. All micr ...

s and detoxification systems in response to harmful environmental molecules. The '' Thermoanaerobacter tengcongensis'' sequenc
AE013027
overlaps with that of

purine riboswitch A purine riboswitch is a sequence of ribonucleotides in certain messenger RNA (mRNA) that selectively binds to purine ligands via a natural aptamer domain. This binding causes a conformational change in the mRNA that can affect translation by rev ...

suggesting that the two

riboswitch In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly in ...

es may work in conjunction to regulate the upstream gene which codes for TTE058
(Q8RC62)
a member of the

permease The permeases are membrane transport proteins, a class of multipass transmembrane proteins that allow the diffusion of a specific molecule in or out of the cell in the direction of a concentration gradient, a form of facilitated diffusion. The per ...

family. Nelson et al. showed that this riboswitch senses and responds to

guanidine Guanidine is the compound with the formula HNC(NH2)2. It is a colourless solid that dissolves in polar solvents. It is a strong base that is used in the production of plastics and explosives. It is found in urine predominantly in patients experi ...

and it was renamed Guanidine-I riboswitch. Furthermore, they demonstrated that bacteria are capable of endogenously producing guanidine and the riboswitch controls genes whose products are involved in modification or pumping out guanidine as a toxic compound from bacteria. Crystal structures of the riboswitch bound to the ligand have also been determined. The mini-ykkC RNA motif is a putative ''cis''-regulatory element that apparently regulates similar

gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

s to those regulated by the Guanidine-I riboswitch (ykkC/yxkD leader). However, the mini-ykkC RNA motif is simpler in structure and has fewer highly conserved

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecul ...

positions than the ykkC-yxkD leader. Despite this each of its two stem-loop structures directly bind free guanidine. Therefore, mini-ykkC RNA motif represents a distinct class of guanidine-sensing RNAs called Guanidine-II riboswitch. Its crystal structure was also determined. 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. 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. Biochemical validation has been presented to show that this motif is a third class of guanidine riboswitches called Guanidine-III riboswitch. ykkC-III-RNA

References

External links

* * {{Rfam, id=RF01763, name=ykkC-III RNA Cis-regulatory RNA elements