HiSCRIBE – A novel DNA writing technology

Monika Raman, PSG College of Technology, Coimbatore

The ability to efficiently and dynamically modify the information contained in genomes would allow for tools to investigate cell biology and govern cell phenotypes effectively. Present DNA writing platforms that are recombineering-mediated DNA writing platforms in bacteria are only available for particular laboratory settings and are not available for in situ applications. 

For example, the SCRIBE technique: For some years, researchers Timothy Lu and Farzadfard have been investigating how DNA may be utilized to store information such as cellular event memory. In 2014, they discovered a means to use bacterias to retain long-term memories of experiences such as chemical exposure using the “genomic tape recorder” via engineering E. coli.

To do this, the researchers engineered the cells to create a retron reverse transcriptase enzyme, which generates single-stranded DNA (ssDNA), as well as a recombinase enzyme, which can insert (“write”) a specific sequence of ssDNA into a particular location in the genome. 

This approach, termed SCRIBE by the scientists, was somewhat inefficient in writing. Out of 10,000 E. coli cells per generation, only one would get the new DNA that researchers were trying to integrate into the cells. They occur partly because E. coli has cellular mechanisms, preventing the accumulation and integration of ssDNA into its genomes. 

Biological engineers at MIT developed a novel technique to effectively alter bacterial genomes and encode memories into bacterial cells by rewriting their DNA to overcome this limitation. 

So, HiSCRIBE is that novel DNA writing technology created by MIT researchers is far more efficient than prior systems. Fahim Farzadfard, a former MIT postdoc and the primary author of this study stated: “Here we built a retroelement-mediated DNA writing system that permits fast and accurate editing of bacterial genomes without the necessity for target-specific elements or selection.”

HiSCRIBE approach

Various types of spatial and temporal information may be permanently stored and retrieved by sequencing the cells’ DNA using this method.

This technique could record cellular interactions or spatial location. According to the researchers, this method can activate, edit, or silence genes in bacteria found in natural communities like the human microbiome.

This approach allows performing genome editing and DNA writing outside of the lab, whether to engineer bacteria, optimize features of interest in situ, or explore evolutionary dynamics and interactions in bacterial communities.

How was the efficiency of HiSCRIBE boosted?

The researchers in the current study attempted to improve the effectiveness by removing some of E.coli’s defensive systems against ssDNA. They started by blocking exonucleases, which are enzymes that break down ssDNA. They also knocked out genes involved in mismatch repair, a mechanism that typically inhibits ssDNA incorporation into the genome.  

The researchers accomplished near-universal integration of the genetic alterations they attempted to introduce with those adjustments, resulting in an unrivalled and effective method for editing bacterial genomes.

“Because of that improvement, we were able to accomplish some applications that we couldn’t do with the prior generation of SCRIBE or other DNA writing technologies,” Farzadfard adds. 

What are the other functions that HiSCRIBE can do?

The researchers showed in their 2014 work that the duration and intensity of exposure to particular molecules may be recorded using SCRIBE. But with the new HiSCRIBE system, they can track such exposures and other sorts of events, such as cell interactions. 

The researchers have shown, for example, that they can monitor a process called bacterial conjugation, during which bacteria exchange parts of DNA. The researchers can detect which cells have interacted by sequencing their DNA to discover which barcodes they contain by incorporating a DNA “barcode” into each cell’s genome, which can then be transferred with other cells. Researchers may use this type of mapping to learn more about how bacteria interact within aggregates like biofilms. 

This method can create a synthetic ecosystem made up of bacteria and bacteriophages that can continually rewrite portions of their genome and evolve at a faster rate than natural evolution would allow. 

This method involves editing the genome of a single bacterial species within a community of several species. In this example, they inserted the gene for a galactose-degrading enzyme into E. coli cells that were growing in a culture containing many other bacterium species. 

Antibiotic-resistant bacteria may also cause the next pandemic, and it’s critical to discover a way to avoid it. As a result, methods like HiSCRIBE, which use species-selective editing, might provide a unique strategy to make antibiotic-resistant bacteria more susceptible to current antibiotics by silencing their resistance genes. However, developing such therapies would most likely take several years of research. 

Also read: Are children of heavy drinkers more exposed to adversities?

Reference: 

• Farzadfard, F., Gharaei, N., Citorik, R. J., & Lu, T. K. (2021). Efficient retroelement-mediated DNA writing in bacteria. Cell Systems, S2405471221002519. https://doi.org/10.1016/j.cels.2021.07.001
• Technology, M. I. of. (n.d.). New method opens the door to efficient genome writing in bacteria. Retrieved August 6, 2021, from https://phys.org/news/2021-08-method-door-efficient-genome-bacteria.html

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About the author: Monika Raman is an undergraduate student pursuing her final year B. Tech in Biotechnology. She is an enthusiastic Biotech student aspiring for an opportunity to develop skills and grow professionally in the research field. Extremely motivated and possess strong interpersonal skills.