RE-BUILD WITH RETRONS

Introduction

Genetic engineering has successfully managed to change the fate of biotechnology. It has opened up our doors towards answers and opportunities.

When we talk about genetic engineering the first thing that comes to our mind is manipulating a gene towards our advantage. As genetic modification takes over all the production fields, new technologies to achieve the desired product come into the picture.



The use of Proteins to modify an organism came to life in Late 1900’s. Then came CRISPR which made editing easy for the scientists and piqued their interests into learning what more could be done.


CRISPR makes “the cut”

CRISPR was discovered in 2009 by Emmanuelle Charpentier and Jennifer Doudna, these women transformed the future of science and were awarded a Nobel Prize for Chemistry in 2020. It involved the process of physically cutting a DNA in order to induce the mutation.





Although the technology has revolutionized the concept of genetic modification, it does seem to have several drawbacks, one of which is to attack off target resulting in formation of undesired products.


RETRONS at home

Around the same time another protein with unknown functions was discovered, it was called “ Retron”. Retrons were commonly associated with prophage DNA and were found in the genomes of a wide variety of different bacteria.

This short satellite RNA molecule located in bacteria was found in 1984. Further studies suggested that these strands consisted of an RNA strand linked to a DNA strand which was later on termed as msDNA. These are linked by a 2’-3’ phosphodiester linkage and the base pairs vary with the organism.


Experiments conducted by Shimamoto.T., Hsu.M.Y., Inouye.S. and Inouye.M. in 1993 were able to help us to come to a conclusion that the DNA segment of this molecule was variable and with arbitrary sequences, it could encode a DNA. Till date there have been 4 major experiments that have lead to the progress in implementation of Retrons which include: -


1. In 1995, Gene regulation by antisense DNA was produced in-vivo by Mao,J.R., Shimada,M., Inouye,S. and Inouye,M.


2. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations conducted by Farzadfard,F. and Lu,T.K. in 2016.


3. Functional genetic variants by precise genome editing by Sharon,E., Chen,S.A., Khosla,N.M., Smith,J.D., Pritchard,J.K. and Fraser,H.B. in 2018


4. Retro-element-based genome editing and evolution in 2018 by Simon, A.J., Morrow, B.R. and Ellington,A.D.


It wasn’t until June 2020 that Rotem Sorek’s group found that the Retron ssDNA detected whether a virus had infected the cell, forming part of the bacterial immune system. Several experiments were conducted by Schubert on E. coli in order to create a desired genetic tweak and it was ultimately achieved.


Retrons were potentially termed as powerful tools for genome editing because they could provide higher copy of intracellular DNAs in orthogonal hosts. While Crispr and other genetic modifications force a cell to take up the changes, Retrons casually introduce it to them as they replicate or repair. RLR have also been found to eliminate the genetic defects that are caused by bacteria making them more reliable. Several efforts are being made of Retrons editing the genomic sequences for several other species.


Retrons have a unique ability to produce sequences in-vivo via the help of satellite DNA. This ability can be used to our benefit as no external resources are required in order to force this result. These can be used as a template to add to a gene as it steps towards its simple survival instinct. Although technologies are yet to be developed, Retrons are the future.



Akanksha Damani

Dept. of Biochemistry and Biotechnology

St. Xavier's College, Ahmedabad



Reference
  1. https://www.pnas.org/content/118/18/e2018181118

  2. https://www.nature.com/articles/s41579-020-00488-2

  3. https://www.biorxiv.org/content/10.1101/2021.05.11.443596v1.full.pdf

  4. https://www.bionews.org.uk/page_156297

  5. https://pubmed.ncbi.nlm.nih.gov/31598685/

  6. https://www.sciencedaily.com/releases/2021/04/210430120411.htm

  7. https://pubmed.ncbi.nlm.nih.gov/16093702/

  8. https://www.sciencedirect.com/topics/neuroscience/genetic-engineering

  9. https://www.genome.gov/about-genomics/policy-issues/what-is-Genome-Editing

  10. https://www.hilarispublisher.com/open-access/crispr-technology-advantages-limitations-and-future-direction.pdf

  11. https://academic.oup.com/nar/article/47/21/11007/5584520#185741781

  12. https://pubmed.ncbi.nlm.nih.gov/30245013/

  13. Farzadfard, F., & Lu, T. K. (2014). Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science, 346(6211).

  14. . Sharon, E., Chen, S. A. A., Khosla, N. M., Smith, J. D., Pritchard, J. K., & Fraser, H. B. (2018). Functional genetic variants revealed by massively parallel precise genome editing. Cell, 175(2), 544-557.

  15. Simon, A. J., Morrow, B. R., & Ellington, A. D. (2018). Retro-element-based genome editing and evolution. ACS synthetic biology, 7(11), 2600-2611.

  16. Mao, J. R., Shimada, M., Inouye, S., & Inouye, M. (1995). Gene Regulation by Antisense DNA Produced in Vivo (∗). Journal of Biological Chemistry, 270(34), 19684-19687.





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