Retron

---

title: "Retron" type: doc version: 1 created: 2026-02-28 author: "Wikipedia contributors" status: active scope: public tags: ["non-coding-rna"] topic_path: "general/non-coding-rna" source: "https://en.wikipedia.org/wiki/Retron" license: "CC BY-SA 4.0" wikipedia_page_id: 0 wikipedia_revision_id: 0

::data[format=table title="Infobox rfam"]

Field	Value
Name	Retron msr RNA
image	RF00170.jpg
caption	Predicted secondary structure and sequence conservation of msr
Symbol	msr
Rfam	RF00170
RNA_type	Gene
Tax_domain	Bacteria
SO
::

| Name = Retron msr RNA | image = RF00170.jpg | caption = Predicted secondary structure and sequence conservation of msr | Symbol = msr | AltSymbols = | Rfam = RF00170 | miRBase = | miRBase_family = | RNA_type = Gene | Tax_domain = Bacteria | GO = | SO = | CAS_number = | EntrezGene = | HGNCid = | OMIM = | PDB = | RefSeq = | Chromosome = | Arm = | Band = | LocusSupplementaryData =

A retron is a distinct DNA sequence found in the genome of many bacteria species that codes for reverse transcriptase and a unique single-stranded DNA/RNA hybrid called multicopy single-stranded DNA (msDNA). Retron msr RNA is the non-coding RNA produced by retron elements and is the immediate precursor to the synthesis of 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 the 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.

Sequence and structure

::figure[src="https://upload.wikimedia.org/wikipedia/commons/4/40/Retron_organization.png" caption="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."] ::

Classification and occurrence

For many years after their discovery in animal viruses, reverse transcriptases were 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: 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.
• diversity-generating retroelements (DGRs). |vauthors=Simon DM, Zimmerly S |title=A diversity of uncharacterized reverse transcriptases in bacteria |journal=Nucleic Acids Res. |volume=36 |issue=22 |pages=7219–7229 |year=2008 |url= |doi=10.1093/nar/gkn867|citeseerx=10.1.1.358.8390 |pmid=19004871 |pmc=2602772 }} The DGRs are not mobile, but function to diversify DNA sequences. |vauthors=Medhekar B, Mille JF |title=Diversity-Generating Retroelements |journal=Current Opinion in Microbiology |volume=10 |issue=4 |pages=388–395 |year=2007 |doi=10.1016/j.mib.2007.06.004 |pmc=2703298 |pmid=17703991}} For example, DGRs mediate the switch between pathogenic and free-living phases of Bordetella. |vauthors=Liu M, Gingery M, Doulatov SR, Liu Y, Hodes A, Baker S, Davis P, Simmonds M, Churcher C, Mungall K, Quail MA, Preston A, Harvill ET, Maskell DJ, Eiserling FA, Parkhill J, Miller JF |title=Genomic and Genetic Analysis of Bordetella Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes |journal=J. Bacteriol. |volume=186 |issue=5 |pages=1503–1517 |year=2004 |doi=10.1128/JB.186.5.1503-1517.2004 |pmc=344406 |pmid=14973019 |bibcode=2004JBact.186.1503L

Function

Since retrons are not mobile, their appearance in diverse bacterial species is not a "selfish DNA" phenomenon. Rather, bacterial retrons confer some protection from phage infection to bacterial hosts. Several retrons are located in DNA regions next to certain protein effector-coding genes. When their expression is activated, most of these effectors and their associated retrons function together to block phage infection.

Retrons in genetic engineering

Retrons have emerged as powerful tools in genetic engineering due to their unique ability to produce single-stranded DNA (ssDNA) inside cells. Here are some of the key ways retrons have been used:

In Situ DNA Production for Genome Editing

Retrons generate ssDNA through reverse transcription of a noncoding RNA. This ssDNA can serve as a donor template for genome editing, for example in recombineering and CRISPR-based systems. This approach allows for precise, targeted mutations without the need to introduce external DNA.

Retron Library Recombineering (RLR)

RLR is a technique that enables massively parallel genome editing. It uses retrons to generate millions of unique mutations simultaneously, each tagged with a molecular "barcode." This allows researchers to:

• Perform high-throughput genetic screens
• Simultaneously modify multiple sites on a single genome
• Study genotype-phenotype relationships
• Track mutations across large populations of cells

Biological Recording

Retrons have been engineered to act as molecular recorders, capturing information about cellular events by integrating specific DNA sequences into the genome. This could be used to monitor gene expression or environmental changes over time.

Reduced Toxicity Compared to CRISPR

Unlike CRISPR-Cas9, which introduces double-stranded breaks (DSBs) that can be toxic or may lead to off-target effects, retron-based editing avoids DSBs, making it a reduced toxicity alternative for certain applications.

Synthetic Biology and Evolutionary Engineering

Retrons are being explored for continuous evolution of synthetic genomes, enabling iterative cycles of mutation and selection to evolve new traits or functions in microbes.

References

References

1. (2005). "Retrons, msDNA, and the bacterial genome". Cytogenet Genome Res.
2. (2022-09-01). "Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems". Nature.
3. (2020). "Bacterial Retrons Function In Anti-Phage Defense". Cell.
4. (2025). "An experimental census of retrons for DNA production and genome editing". Nature Biotechnology.
5. (2019). "Retrons and their applications in genome engineering". Nucleic Acids Research.
6. (2024). "Retron Library Recombineering: Next Powerful Tool for Genome Editing after CRISPR/Cas". ACS Synthetic Biology.
7. (2024). "Simultaneous multi-site editing of individual genomes using retron arrays". Nature Chemical Biology.
8. (2024). "Toward DNA-Based Recording of Biological Processes". Int. J. Mol. Sci..
9. (2021). "High-throughput functional variant screens via in vivo production of single-stranded DNA". Proc. Natl. Acad. Sci..
10. (2022). "Bacterial Retrons Enable Precise Gene Editing in Human Cells". The CRISPR Journal.
11. (2022). "High-efficiency retron-mediated single-stranded DNA production in plants". Synthetic Biology.
12. (2022). "Efficient and iterative retron-mediated in vivo recombineering in Escherichia coli". Synthetic Biology.
13. (2023). "Retron-mediated multiplex genome editing and continuous evolution in Escherichia coli". Nucleic Acids Research.

::callout[type=info title="Wikipedia Source"] This article was imported from Wikipedia and is available under the Creative Commons Attribution-ShareAlike 4.0 License. Content has been adapted to SurfDoc format. Original contributors can be found on the article history page. ::