The ‘Bacteria’s Movie Out’: cas9 CRISPR in genomic encoding

Rafat Shahriar Islam

DNA (Deoxyribonucleic acid), the genetic blueprint of every living creature including diverse classes of microorganisms has its sole act to carry the inheritance in sequences of generation. A bacteria, much like a prokaryotic tiny microbe, has been used by the researchers of Harvard Medical School after harnessing its DNA  being used as a synthetic raw material to store information digitally in an In vitro(Outside of living cells) process.

CRISPR (Clustered regularly interspaced short palindromic repeats), a prokaryotic DNA of Bacterial genome provides the bacterial genome an acquired immunity against viral phage or plasmid. In a palindromic repeat, having same nucleotide sequence in both directions, there are repeated short spacer DNA segments along with small clusters of cas genes are located next to CRISPR sequences (CRISPR/Cas system).  For clear understanding, in CRISPR/Cas9 system, Cas9 nuclease complexes with a synthetic guide RNA (gRNA) cut the genome of a cell, allowing the introduction of genes or snipping out of them.

The researchers at Harvard Medical School described through ‘Cryo-electron microscopy’ that the CRISPR complex loads target DNA and make it ready for cutting by the Cas3 enzyme. These structures reveal a process with multiple layers of error detection preventing unintended genomic damage. Discovered not so many years ago, CRISPR-Cas is an adaptive defense mechanism against viral invaders. In this process, bacteria capturing portions of viral DNA, which are then integrated into its genome producing short RNA sequences known as crRNA (CRISPR RNA). These small crRNA parts are a tool for detecting “enemy” presence.

Acting like a barcode, crRNA complexes with the CRISPR family of enzymes, which together perform the function of ‘border guards’ that move around the bacteria and checks for foreign code. If crRNA/CRISPR complexes encounter genetic material that matches its crRNA, they slice down that DNA to make it harmless. Likewise, as previously told, CRISPR/Cas9 can be programmed with synthetic RNA (gRNA) in order to cut genomes at a specific locus, allowing researchers to edit genes easier than ever.

Now the question may emerge on what if by using CRISPR/Cas system, large populations of the bacterial genome can be used as a biological hard drive that can record information as megabytes/gigabytes like external drives and that can be accessed anytime? Such a breathtaking approach by the researchers of the Wyss Institute of Harvard Medical School have already created an outstanding dimension after engineering a new memory-recording device via genome of bacteria population in a chronological fashion.

The first approach began recently in 2016 by an Engineering team led by George Church from Harvard Medical School and the Wyss Institute to build the first molecular recorder based on CRISPR system where bacteria are encoded bits of information within their DNA to produce a memory of that information within the genome as a cellular model. The information is stored as an array of sequences in the CRISPR locus which whenever required can be recalled and can be used to reconstruct a still or moving image!

In July 12, 2016, in Nature, the same team showed the first of its kind approach to a whole new level showing that they were able to encode a digitized image of a galloping horse in bacterial living cells which were one of the first ever reminiscent hand-made paintings crafted on the cave wall by ancient humans. It was of one of the first motion pictures ever made by the team successfully!

To explain briefly, the CRISPR system captures viral DNA molecules and generates short, so-called ‘spacer’ sequences from them that are added as new elements continuously in a growing sequence located in the CRISPR locus of bacterial genomes. The CRISPR-Cas9 protein constantly resorts to this memory to destroy the same viruses if relapsed.

In this study, it was shown that two proteins of the CRISPR system, cas1, and cas2 that was engineered into a molecular recording tool enabling the scaled-up potential for acquiring memories in the genome. Natural tissue environments can also be recorded presenting a way to cure different types of living cells where they synthetically create memory hotspots in their genomes.

On much larger scales, the team worked on both still and moving images because they represent clearly defined data were developing this concept for making a movie offers the chance to have bacteria gather information frame-wise over time.

The study’s first author Shipman described that they had translated the digital information contained in each pixel of an image into a DNA code that also incorporated spacers making each frame a collection of these. The author further added that later they had provided spacer collections for each consecutive frame chronologically to a population of bacteria using Cas1/Cas2 activity, adding them to the CRISPR arrays in bacterial genomes after they had retrieved all arrays by DNA sequencing. Finally, a reconstructed image using all frames of the galloping horse movie was screened in a sequential order of appearance.

Another researcher Min Luo, working on CRISPR/cas system stated that these steps must occur in a precise order. Luo further replied that evolutionarily, this mechanism has to ensure that this complex must degrade only invading viral DNA.

In future, the team will focus on inventing a new molecular recorder to memorize biological information in other types of the cell too. Donald Ingber, Wyss founding director addressed this as the ‘groundbreaking technology’ in the field of ‘DNA-based information storage’ aiding the living cells to record, archive and propagate that information to study dynamic biological processes in an in vivo (inside the living body) way which is also another example of ‘bio-inspired engineering’.

In fine, Shipman forecast about their invention, “One day, we may be able to follow all the developmental decisions that a differentiating neuron is taking from an early stem cell to a highly specialized type of cell in the brain, leading to a better understanding of how basic biological and developmental processes are choreographed”.

Rafat Shahriar Islam, is a graduate from Department of Pharmacy, East West University.  He can be reached at rafat.islam46@gmail.com

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