Asd RNA motif
Encyclopedia
The asd RNA motif is a conserved RNA
structure found is certain lactic acid bacteria
. The asd motif was detected by bioinformatics
and an individual asd RNA in Streptococcus pyogenes
was detected by microarray
and northern hybridization experiments as a 170-nucleotide molecule called "SR914400". The transcription start site determined for SR914400 corresponds to the 5′-end of the molecule shown in the consensus diagram.
Some asd RNAs are associated with genes, such as asd, that are suggestive of a cis-regulatory function
. However, several lines of evidence suggest that this is not the biological role of asd RNAs. First, in some cases, the asd RNA is not in the 5' untranslated region of any annotated gene
. Second, in Streptococcus mutans
, there is a strong promoter immediately downstream of the transcription terminator that follows the asd RNA, and this promoter precedes the downstream gene. This arrangement suggests that asd RNA transcription is terminated, and the gene is transcribed from the downstream promoter. Finally, although the asd gene encodes an enzyme, aspartate-semialdehyde dehydrogenase
, that participates in the synthesis of methionine
, lysine
and threonine
, transcription levels of the asd gene remain constant even when the concentrations of these amino acids are varied.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
structure found is certain lactic acid bacteria
Lactic acid bacteria
The lactic acid bacteria comprise a clade of Gram-positive, low-GC, acid-tolerant, generally non-sporulating, non-respiring rod or cocci that are associated by their common metabolic and physiological characteristics. These bacteria, usually found in decomposing plants and lactic products, produce...
. The asd motif was detected by bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
and an individual asd RNA in Streptococcus pyogenes
Streptococcus pyogenes
Streptococcus pyogenes is a spherical, Gram-positive bacterium that is the cause of group A streptococcal infections. S. pyogenes displays streptococcal group A antigen on its cell wall. S...
was detected by microarray
Microarray
A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate that assays large amounts of biological material using high-throughput screening methods.Types of microarrays include:...
and northern hybridization experiments as a 170-nucleotide molecule called "SR914400". The transcription start site determined for SR914400 corresponds to the 5′-end of the molecule shown in the consensus diagram.
Some asd RNAs are associated with genes, such as asd, that are suggestive of a cis-regulatory function
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...
. However, several lines of evidence suggest that this is not the biological role of asd RNAs. First, in some cases, the asd RNA is not in the 5' untranslated region of any annotated 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...
. Second, in Streptococcus mutans
Streptococcus mutans
Streptococcus mutans is a facultatively aerobic, Gram-positive coccus-shaped bacterium commonly found in the human oral cavity and is a significant contributor to tooth decay.The microbe was first described by J Kilian Clarke in 1924.-Introduction:...
, there is a strong promoter immediately downstream of the transcription terminator that follows the asd RNA, and this promoter precedes the downstream gene. This arrangement suggests that asd RNA transcription is terminated, and the gene is transcribed from the downstream promoter. Finally, although the asd gene encodes an enzyme, aspartate-semialdehyde dehydrogenase
Aspartate-semialdehyde dehydrogenase
In enzymology, an aspartate-semialdehyde dehydrogenase is an enzyme that is very important in the biosynthesis of amino acids in prokaryotes, fungi, and some higher plants. It forms an early branch point in the metabolic pathway forming lysine, methionine, leucine and isoleucine from aspartate...
, that participates in the synthesis of methionine
Methionine
Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...
, lysine
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
and threonine
Threonine
Threonine is an α-amino acid with the chemical formula HO2CCHCHCH3. Its codons are ACU, ACA, ACC, and ACG. This essential amino acid is classified as polar...
, transcription levels of the asd gene remain constant even when the concentrations of these amino acids are varied.