The ''psaA'' RNA motif describes a class of

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

s with a common

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

. ''psaA'' RNAs are exclusively found in locations that presumably correspond to the

5' untranslated region The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly Upstream and downstream (DNA), upstream from the initiation codon. This region is im ...

s of

operon In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splic ...

s formed of ''psaA'' and ''psaB''

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 ba ...

s. For this reason, it was hypothesized that ''psaA'' RNAs function as

cis-regulatory element ''Cis''-regulatory elements (CREs) or ''Cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphoge ...

s of these genes. The ''psaAB'' genes encode

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s that form subunits in the

photosystem I Photosystem I (PSI, or plastocyanin–ferredoxin oxidoreductase) is one of two photosystems in the photosynthetic light reactions of algae, plants, and cyanobacteria. Photosystem I is an integral membrane protein complex that uses ...

structure used for

photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...

. ''psaA'' RNAs have been detected only in

cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blu ...

, 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 In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The fu ...

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 may refer to: Politics and ideology Politics *Radical politics, the political intent of fundamental societal change *Radicalism (historical), the Radical Movement that began in late 18th century Britain and spread to continental Europe and ...

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 intramolecular base pairing is a pattern that can occur in single-stranded 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 ...

s are terminated by the stable UNCG

tetraloop Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. There are many variants of the tetraloop. The published ones include ANYA, CUYG, GNRA, UNAC and UNCG. Three types of tetraloops are ...

. 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.

References

External links

* {{Rfam, id=RF01752, name=psaA RNA Cis-regulatory RNA elements