PsaA RNA motif
Encyclopedia
The psaA RNA motif describes a class of RNA
s with a common secondary structure
. psaA RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operon
s formed of psaA and psaB gene
s. For this reason, it was hypothesized that psaA RNAs function as cis-regulatory element
s of these genes. The psaAB genes encode protein
s that form subunits in the photosystem I
structure used for photosynthesis
. psaA RNAs have been detected only in cyanobacteria, which is consistent with their association with photosynthesis.
psaAB genes are known to be regulated in species of cyanobacteria that do not use psaA RNAs, and this system of regulation involves transcription factor
proteins. In this system, the expression of psaAB genes is increased when cells are growing with limited amount of light, presumably to maximize their energy from the limited resource. On the other hand, the genes' expression is reduced when light levels are high, presumable to reduce damage that can be caused by free radical
s that are a byproduct of photosynthesis. A region of the psaA RNA motif corresponds to the expected sequence of a binding site of the NtcA protein, which is involved in nitrogen regulation.
Structurally, the psaA RNA motif consists of a somewhat complex arrangement of stems resulting from base pairing, and many stem-loop
s are terminated by the stable UNCG tetraloop
. Most of the conserved nucleotides in the motif participate in standard Watson-Crick base pairs. However, since the precise function of psaA RNAs is unknown, it is also unknown what biochemical role these features play.
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
s with a common secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
. psaA RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operon
Operon
In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo trans-splicing to create...
s formed of psaA and psaB 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. For this reason, it was hypothesized that psaA RNAs function as cis-regulatory element
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...
s of these genes. The psaAB genes encode protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s that form subunits in the photosystem I
Photosystem I
Photosystem I is the second photosystem in the photosynthetic light reactions of algae, plants, and some bacteria. Photosystem I is so named because it was discovered before photosystem II. Aspects of PS I were discovered in the 1950s, but the significances of these discoveries was not yet known...
structure used for photosynthesis
Photosynthesis
Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...
. psaA RNAs have been detected only in cyanobacteria, which is consistent with their association with photosynthesis.
psaAB genes are known to be regulated in species of cyanobacteria that do not use psaA RNAs, and this system of regulation involves transcription factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
proteins. In this system, the expression of psaAB genes is increased when cells are growing with limited amount of light, presumably to maximize their energy from the limited resource. On the other hand, the genes' expression is reduced when light levels are high, presumable to reduce damage that can be caused by free radical
Radical (chemistry)
Radicals are atoms, molecules, or ions with unpaired electrons on an open shell configuration. Free radicals may have positive, negative, or zero charge...
s that are a byproduct of photosynthesis. A region of the psaA RNA motif corresponds to the expected sequence of a binding site of the NtcA protein, which is involved in nitrogen regulation.
Structurally, the psaA RNA motif consists of a somewhat complex arrangement of stems resulting from base pairing, and many 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 are terminated by the stable UNCG tetraloop
Tetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG. The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3'...
. Most of the conserved nucleotides in the motif participate in standard Watson-Crick base pairs. However, since the precise function of psaA RNAs is unknown, it is also unknown what biochemical role these features play.