Mini-ykkC RNA motif
Encyclopedia
The mini-ykkC RNA motif is a putative RNA
structure that is conserved in bacteria
. The motif consists of two conserved stem-loop
s 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 phyla of bacteria. It is expected that the RNAs are cis-regulatory elements, because they are typically located upstream of protein-coding gene
s.
The genes that are apparently controlled by mini-ykkC RNAs bear a resemblance to the genes controlled by another putative cis-regulatory RNA element called the ykkC-yxkD leader
, and nine gene families are common to both. Therefore, it was proposed that these two RNA classes have the same function. However, their mechanisms might be different. While the complex structure and many conserved nucleotides found in the ykkC-yxkD leader suggest that it might be a riboswitch
, these features are not present in the mini-ykkC RNA motif.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure that is conserved in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
. The motif consists of two conserved stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
s whose terminal loops contain the RNA sequence ACGR, where R represents either A or G. Mini-ykkC RNAs are widespread in Proteobacteria
Proteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....
, but some are predicted in other phyla of bacteria. It is expected that the RNAs are cis-regulatory elements, because they are typically located upstream of protein-coding 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.
The genes that are apparently controlled by mini-ykkC RNAs bear a resemblance to the genes controlled by another putative cis-regulatory RNA element called the ykkC-yxkD leader
YkkC-yxkD leader
The YkkC/YxkD leader is a conserved RNA structure found upstream of the ykkC and yxkD genes in Bacillus subtilis 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...
, and nine gene families are common to both. Therefore, it was proposed that these two RNA classes have the same function. However, their mechanisms might be different. While the complex structure and many conserved nucleotides found in the ykkC-yxkD leader suggest that it might be a 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...
, these features are not present in the mini-ykkC RNA motif.