The "psaA" RNA motif describes a class of RNAs with a common secondary structure. "psaA" RNAs are exclusively found in locations that presumably correspond to the 5' untranslated regions of operons formed of "psaA" and "psaB" genes. For this reason, it was hypothesized that "psaA" RNAs function as cis-regulatory elements of these genes. The "psaAB" genes encode proteins 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 radicals 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-loops 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.
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