MIT scientists have actually created a method to program memories into bacterial cells by rewording their DNA more effectively. Credit: MIT News, iStockphoto
Technique for modifying bacterial genomes can tape-record interactions in between cells, might use a method to modify genes in the human microbiome.
Biological engineers at MIT have actually created a brand-new method to effectively modify bacterial genomes and program memories into bacterial cells by rewording their DNA. Using this method, different kinds of spatial and temporal info can be completely saved for generations and recovered by sequencing the cells’ DNA.
The brand-new DNA writing strategy, which the scientists call HiSCRIBE, is far more effective than formerly established systems for modifying DNA in germs, which had a success rate of just about 1 in 10,000 cells per generation. In a brand-new research study, the scientists showed that this method might be utilized for keeping memory of cellular interactions or spatial place.
This strategy might likewise make it possible to selectively modify, trigger, or silence genes in particular types of germs residing in a natural neighborhood such as the human microbiome, the scientists state.
“With this new DNA writing system, we can precisely and efficiently edit bacterial genomes without the need for any form of selection, within complex bacterial ecosystems,” states Fahim Farzadfard, a previous MIT postdoc and the lead author of the paper. “This enables us to perform genome editing and DNA writing outside of laboratory settings, whether to engineer bacteria, optimize traits of interest in situ, or study evolutionary dynamics and interactions in the bacterial populations.”
Timothy Lu, an MIT partner teacher of electrical engineering and computer technology and of biological engineering, is the senior author of the research study, which was released on August 5, 2021, in Cell Systems. Nava Gharaei, a previous college student at Harvard University, and Robert Citorik, a previous MIT college student, are likewise authors of the research study.
Genome composing and taping memories
For numerous years, Lu’s laboratory has actually been dealing with methods to utilize DNA to save info such as memory of cellular occasions. In 2014, he and Farzadfard established a method to utilize germs as a “genomic tape recorder,” engineering E. coli to save long-lasting memories of occasions such as a chemical direct exposure.
To attain that, the scientists crafted the cells to produce a reverse transcriptase enzyme called retron, which produces a single-stranded DNA (ssDNA) when revealed in the cells, and a recombinase enzyme, which can place (“write”) a particular series of single-stranded DNA into a targeted website in the genome. This DNA is produced just when triggered by the existence of an established particle or another kind of input, such as light. After the DNA is produced, the recombinase inserts the DNA into a preprogrammed website, which can be throughout the genome.
That strategy, which the scientists called SCRIBE, had a reasonably low composing effectiveness. In each generation, out of 10,000 E. coli cells, just one would obtain the brand-new DNA that the scientists attempted to include into the cells. This remains in part since the E. coli have cellular systems that avoid single-stranded DNA from being collected and incorporated into their genomes.
In the brand-new research study, the scientists attempted to enhance the effectiveness of the procedure by removing a few of E. coli’s defense reaction versus single-stranded DNA. First, they disabled enzymes called exonucleases, which break down single-stranded DNA. They likewise knocked out genes associated with a system called inequality repair work, which usually avoids combination of single-stranded DNA into the genome.
With those adjustments, the scientists had the ability to attain near-universal incorporation of the hereditary modifications that they attempted to present, developing an unequaled and effective method for modifying bacterial genomes without the requirement for choice.
“Because of that improvement, we were able to do some applications that we were not able to do with the previous generation of SCRIBE or with other DNA writing technologies,” Farzadfard states.
Cellular interactions
In their 2014 research study, the scientists revealed that they might utilize SCRIBE to tape-record the period and strength of direct exposure to a particular particle. With their brand-new HiSCRIBE system, they can trace those type of direct exposures in addition to extra kinds of occasions, such as interactions in between cells.
As one example, the scientists revealed that they might track a procedure called bacterial conjugation, throughout which germs exchange pieces of DNA. By incorporating a DNA “barcode” into each cell’s genome, which can then be exchanged with other cells, the scientists can figure out which cells have actually communicated with each other by sequencing their DNA to see which barcodes they bring.
This sort of mapping might assist scientists study how germs interact with each other within aggregates such as biofilms. If a comparable method might be released in mammalian cells, it might one day be utilized to map interactions in between other kinds of cells such as nerve cells, Farzadfard states. Viruses that can cross neural synapses might be set to bring DNA barcodes that scientists might utilize to trace connections in between nerve cells, using a brand-new method to assist map the brain’s connectome.
“We are using DNA as the mechanism to record spatial information about the interaction of bacterial cells, and maybe in the future, neurons that have been tagged,” Farzadfard states.
The scientists likewise revealed that they might utilize this strategy to particularly modify the genome of one types of germs within a neighborhood of lots of types. In this case, they presented the gene for an enzyme that breaks down galactose into E. coli cells growing in culture with numerous other types of germs.
This sort of species-selective modifying might use an unique method to make antibiotic-resistant germs more vulnerable to existing drugs by silencing their resistance genes, the scientists state. However, such treatments would likely need numerous years more years of research study to establish, they state.
The scientists likewise revealed that they might utilize this strategy to craft an artificial environment made from germs and bacteriophages that can constantly reword particular sections of their genome and develop autonomously with a rate greater than would be possible by natural advancement. In this case, they had the ability to enhance the cells’ capability to take in lactose usage.
“This approach could be used for evolutionary engineering of cellular traits, or in experimental evolution studies by allowing you to replay the tape of evolution over and over,” Farzadfard states.
Reference: “Efficient retroelement-mediated DNA writing in bacteria” by Fahim Farzadfard, Nava Gharaei, Robert J. Citorik and Timothy K. Lu, 5 August 2021, Cell Systems.
DOI: 10.1016/j.cels.2021.07.001
The research study was moneyed by the National Institutes of Health, the Office of Naval Research, the National Science Foundation, the Defense Advanced Research Projects Agency, the MIT Center for Microbiome Informatics and Therapeutics, the NSF Expeditions in Computing Program Award, and the Schmidt Science Fellows Program.
