Retron msr RNA is a non-coding RNA produced by retron elements. It is the immediate precursor to the synthesis of a multi-copy extra-chromosomal (satellite) DNA present in many bacteria called multicopy single-stranded DNA (msDNA). The retron msr RNA folds into a characteristic secondary structure that contains a conserved guanosine residue at the end of a stem loop. Synthesis of DNA by a retron-encoded reverse transcriptase (RT) results in a DNA-RNA chimera which is composed of small single-stranded DNA linked to small single-stranded RNA. The RNA strand is joined to the 5' end of the DNA chain via a 2'-5' phosphodiester linkage that occurs from the 2' position of the conserved internal guanosine residue.
Retron elements are about 2 kb long. They contain a single operon controlling the synthesis of an RNA transcript carrying three loci, msr, msd, and ret, that are involved in msDNA synthesis. The DNA portion of msDNA is encoded by the msd gene, the RNA portion is encoded by the msr gene, while the product of the ret gene is a reverse transcriptase similar to the RTs produced by retroviruses and other types of retroelements. Like other reverse transcriptases, the retron RT contains seven regions of conserved amino acids (labeled 1-7 in the figure), including a highly conserved tyr-ala-asp-asp (YADD) sequence associated with the catalytic core. The ret gene product is responsible for processing the msd/msr portion of the RNA transcript into msDNA.
For many years after their discovery in animal viruses, reverse transcriptase was believed to be absent from prokaryotes. Currently, however, RT-encoding elements, i.e. retroelements, have been found in a wide variety of different bacteria. Retrons were the first family of retroelement discovered in bacteria; the other two families of known bacterial retroelements are group II introns and diversity-generating retroelements (DGRs). Group II introns are the best characterized bacterial retroelement and the only type known to exhibit autonomous mobility; they consist of an RT encoded within a catalytic, self-splicing RNA structure. Group II intron mobility is mediated by a ribonucleoprotein comprising an intron lariat bound to two intron-coded proteins. The second family of bacterial retroelement, DGRs, are not mobile, but function to diversify DNA sequences. For example, DGRs mediate the switch between pathogenic and free-living phases of Bordetella.
Since retrons are not mobile, their appearance in diverse bacterial species is not a "selfish DNA" phenomenon. Rather, retrons must confer some selective advantage to the host organism. What this advantage may be is unknown. Except for producing msDNA, no clear phenotype has been associated with them. Despite considerable investigation, very little is known about the function of msDNA, the mobility of retron elements, or their effect on the host cell.