On Retrons

We reprint this article from Habib Maroon’s blog Biobabel, with his kind permission.

by Habib Maroon

The secondary structure of msDNA Ec73. The
76 nt RNA (in box), is joined to a 73nt ssDNA.
Note the 2'-5 phosphodiester bond connecting
the two molecules at the branching guanosine.

Retrons are an understudied type of prokaryotic retroelement responsible for the synthesis of an enigmatic species of small extra-chromosomal satellite DNA termed multicopy single-stranded DNA (msDNA). msDNAs are actually composed of both a single-stranded (ss) DNA and a ssRNA. The 5' end of the msDNA is covalently bonded to an internal guanosine residue of the msRNA by a unique 2'-5' phosphodiester bond, whilst the 3' ends of the molecules are joined by a small stretch of base-pairing. msDNAs are therefore a sort of looped hybrid molecule, but extensive internal base pairing creates various stem-loop/hairpin secondary structures (see figure). The retron, (i. e., the genetic loci encoding the msRNA and msDNA molecules (msr and msd) and the gene encoding the reverse transcriptase (ret) responsible for the synthesis of msDNA) is transcribed as an operon.

Retrons are present in a wide variety of eubacterial, and some archaeal, genomes. A recent study identified 97 different retron-like reverse transcriptase genes within bacteria, however their distribution is sporadic. For instance, seven distinct retron elements have been found amongst E. coli strains, but only 15% of natural E. coli isolates produce msDNAs. Based on their sporadic occurrence and analysis of codon usage, retrons have been suggested to be a recent addition to the E. coli genome.

A major exception to the sporadic distribution found in most bacteria is within the myxobacteria, where all ten genera include msDNA-producing species. Myxobacterial retrons form a phylogenetically related group. These features, as well as sequence divergence, suggest that the common ancestor of the extant myxobacteria contained a retron as much as 150 million years ago, which has been vertically transmitted.

Retrons have not been shown to be mobile genetic elements, although the presence of reverse transcriptase does suggest this possibility. A clue to their propagation is the association of many of them with prophage sequences, suggesting their spread could be associated with bacteriophage. However, as with many observations about retrons, there are plenty of exceptions.

Organisation of a retron operon. Note the inverse orientations and short
overlap of msr and msd.

msDNA is essentially a cDNA produced from a short region of an mRNA template. During msDNA synthesis, an RNA template derived from the operon mRNA and composed of msr and msd, is folded into a specific secondary structure due to flanking inverted repeat sequences. The msd sequence is then reverse transcribed by the retron reverse transcriptase, using the 2'OH group of the 'branching' guanosine residue as a primer. The lagging RNA template strand is then degraded by RNaseH activity (probably host cell derived), leaving the msDNA covalently bonded at it's 5' end and base paired to the msRNA at their 3' ends.

No function has been unequivocally attributed to msDNA. Mutating retron ret genes to prevent synthesis of E. coli or myxococcal msDNAs produces no detectable effects. Overexpression of certain E. coli msDNAs has been shown to increase mutation rate. msDNAs generally form hairpin structures by complementary base pairing of inverted repeat sequences (see figure). However, in many msDNA hairpins the base pairing is imperfect. It appears that the overexpression associated mutation rate phenotype is due to mismatch-containing msDNAs sequestering the mismatch repair enzyme MutS. Overexpression of msDNAs without mismatch-containing hairpins does not cause similar effects. It is possible that msDNA could be regulating MutS availability by this titration mechanism in normal conditions or as part of a stress response. However, the overexpression experiments lead to msDNA concentrations far beyond normal physiological levels, so can yield no more than hints of normal function.

Studies on retrons from Vibrio cholerae suggest potentially important roles for msDNAs. Epidemic cholera is caused by V. cholerae serotypes O1 and O139, both of which contain the retron Vc95. Non-O1, non-O139 strains rarely contain Vc95. This retron is not associated with the CTXphi prophage that encodes cholera toxin, however it's presence correlates with pathogenicity. Interestingly, the genomic location of Vc95 is occupied by other species of retron or by insertions of non-coding sequences in other V. cholerae strains. This implies that retrons are indeed mobile elements, however analysis of this site has not yielded many clues about potential mechanisms of integration or excision.

In conclusion, the lacunae in our understanding of retrons and msDNA are far more striking than the known facts. Are retrons parasitic elements? Or do msDNAs have physiological roles in their host cells? Are retrons mobile elements? Just what does msDNA do? Judging from the literature, interest in retrons peaked around 1990, and recent years have been very fallow. I do hope that funding agencies and researchers keep pursuing the answers to these questions and don't let them remain as an interesting oddity in the literature.

Lampson, B., Inouye, M., & Inouye, S. (2005). Retrons, msDNA, and the bacterial genome. Cytogenetic and Genome Research, 110 (1-4), 491-499 DOI: 10.1159/000084982

Simon, D., & Zimmerly, S. (2008). A diversity of uncharacterized reverse transcriptases in bacteria. Nucleic Acids Research, 36 (22), 7219-7229 DOI: 10.1093/nar/gkn867

Inouye, K., Tanimoto, S., Kamimoto, M., Shimamoto, T., & Shimamoto, T. (2011) Two novel retron elements are replaced with retron-Vc95 in Vibrio cholerae. Microbiology and Immunology, 55(7), 510-513. DOI: 10.1111/j.1348-0421.2011.00342.x

Comments

[Nick Heng]

This is my first visit to Small Things Considered and I find an article on retrons. It brings back good memories because I wrote an elective essay about msDNA/retrons in 1991 (as a third-year undergraduate student) due to its highly unusual structure, and possibly the first instance of retrotransposition in prokaryotes. Back then, its role(s) was unknown and, 20+ years down the track, is still pretty much the same except for the fascinating link between the retron and cholera pathogenesis. Thank you for the article and for maintaining such a great blogging site!