When a bacterium was smarter than a scientist

Just after breakfast, sitting in his laboratory at the University of Alicante, Francisco Mojica stared at his computer screen in dismay. It was the 1990s, and he had just created a database of DNA sequences of extreme bacteria—organisms that lived in conditions that would kill almost any other life. These bacteria inhabited salt-saturated lakes—organisms adapted to be “salt lovers,” as their scientific name, halobalilia, implied.labiotech+1

But instead of the usual, orderly DNA sequences he expected, Mojica stumbled upon something strange: regularly repeated DNA fragments, separated by spaces with ever-changing sequences . They were like repeated words in a strange verse—”word-space-word-space-word.” Interesting. Almost like an archive. But an archive of what?wikipedia

Little did he know that he had just discovered one of the most groundbreaking technologies that would fundamentally revolutionize medicine, agriculture, and biology over the next two decades.

First Spark: The Strange Sequence from 1987

The history of CRISPR (acronym for Clustered Regularly Interspaced Short Palindromic Repeats) begins earlier, in Japan.bitesizebio

In 1987, while working on the gene encoding alkaline phosphatase in E. coli , Japanese scientist Yoshizumi Ishino and his team had an unexpected surprise. While cloning DNA for an experiment, they stumbled upon fragments of DNA that were repeated—a highly unusual finding. These sequences were organized into clusters and were regularly distributed along the bacterial genome.biocompare+1

Ishino and his team published their observations, but their significance was never fully explored. This discovery languished in the scientific literature, like a hidden treasure waiting for adventurers.biocompare

The Key to the Puzzle: Francisco Mojica Discovers the Function

Flash forward to the year 2000. Francisco Mojica, now a researcher at the University of Alicante, was working on a different question: how do bacteria from extreme environments adapt to changes in salt concentration? But his curiosity quickly veered elsewhere.labiotech

Using access to growing genetic databases, he began comparing these strange, repetitive sequences Ishino had previously discovered. Imagine his surprise when he discovered that the same repeats appeared in the genomes of bacteria studied around the world—in microorganisms from the ocean, soil, and caves .biocompare

In 2000, he and his colleagues published work showing that this cluster was highly evolutionarily conserved—and therefore must have meant something important. Its very preservation over millions of years of evolution indicated that nature does nothing without reason.biocompare

But that was just the beginning.

Eureka Moment: Virus in Bacterial DNA

A few years later, while comparing databases, Mojica noticed something extraordinary: DNA fragments nested between repeats in the bacterial genome were identical to fragments of the genomes of viruses (bacteriophages) that attack bacteria .labiotech

Not just any fragments – but fragments of actual viruses infectious to those same bacteria!

It was an immediately logical presumption: if a bacterium stores fragments of a virus’s DNA in its cell, it must have acquired this genetic material somehow . And if it holds them, it must need them for something.labiotech

Mojica hypothesized: CRISPR is a bacteria’s adaptive immune system . Once a virus attacks a bacterium and it becomes infected, part of the virus’s genome is squeezed into the CRISPR archive. The next time the same virus tries to attack that bacterium (or its descendants), the immune system will “remember” it and attack it.wikipedia+1

Sounds almost like memory? Because that’s exactly what it is— biological, genetic memory .

A path through the groves of scientific journals

In 2003, Mojica wrote a paper proposing this theory. He submitted it to Nature , one of the world’s most prestigious scientific journals. It was rejected. He tried the Proceedings of the National Academy of Sciences . It was rejected.wikipedia

Then Molecular Microbiology . Refusal.wikipedia

Nucleic Acids Research . Once again – refusal.wikipedia

He was frustrated, but he didn’t give up. The paper finally made it to the Journal of Molecular Evolution in February 2005. It wasn’t Nature, but it was a publication. Importantly, that same year, independently of Mojica’s work, another laboratory published similar findings.flagshippioneering+1

But something changed. Scientists began to listen.

Experimental Proof: Horvath and Siksnys Show It Works

Although Mojica proposed the hypothesis, experimental evidence came from a completely different direction – from laboratories that were studying… ferments for yogurt production.pmc.ncbi.nlm.nih

In 2005, Philippe Horvath’s team at Danisco (yes, the dairy giant!) investigated how Streptococcus thermophilus bacteria – used to produce yogurt and cheese – could be resistant to infectious viruses (bacteriophages).pmc.ncbi.nlm.nih

Horvath and his colleagues demonstrated experimentally what Mojica had proposed theoretically: when S. thermophilus was infected with a new bacteriophage, the bacterium integrated new sequences derived from the phage’s genome directly into its CRISPR region of DNA . Even better, the next time the same phage tried to infect descendants of that bacterium, they were resistant.pmc.ncbi.nlm.nih

This was not just a theory – it was experimental proof of a working biological immune system.pmc.ncbi.nlm.nih

Separately, that same year, Vytautas Siksnys from Lithuania published a paper showing that the CRISPR system from one bacterium ( S. thermophilus ) could be transferred to a completely different species— E. coli —and it would work there. This was important because it demonstrated the universality of the system.flagshippioneering

2006-2011: Developing the Foundation

In the following years, scientists around the world began to study CRISPR in more detail. Fiona Barrangou and others demonstrated exactly how CRISPR works—how bacteria “learn” to recognize viruses and use this knowledge to protect themselves.nature

Several variants of CRISPR systems have been discovered – CRISPR-Cas9 , CRISPR-Cas12a , and others. Each system had its own Cas proteins – enzymes that perform the actual “cutting” of DNA.pmc.ncbi.nlm.nih

It turned out that Cas9 , from Streptococcus pyogenes (the bacterium that causes angina), was particularly remarkable. When prompted by guide RNA, it would precisely cut DNA exactly where instructed.pmc.ncbi.nlm.nih

By 2011, scientists knew almost everything they needed to know about CRISPR in nature. But no one had yet considered: what if, instead of letting bacteria do what they do naturally, we scientists taught Cas9 to do what we wanted?

The San Juan Meeting and the History That Was Written

In 2011, at a scientific conference in San Juan, Puerto Rico, two scientists from different sides of the Atlantic met by chance.pmc.ncbi.nlm.nih

Jennifer Doudna , a protein structuralist at the University of California, Berkeley, specialized in studying biological mechanisms at the molecular level. Emmanuelle Charpentier , a microbiologist at Umeå University in Sweden, also studied bacterial immune systems.innovativegenomics+1

They talked about CRISPR. Doudna was fascinated; Charpentier was an expert. They decided to collaborate.pmc.ncbi.nlm.nih

2011: Charpentier Discovers the Third Missing Piece

Before Doudna and Charpentier deepened their collaboration, Charpentier had made a significant discovery in her Umeå lab. She was studying CRISPR with Streptococcus pyogenes and discovered something that would change everything.mpg

It turned out that in addition to krRNA (CRISPR RNA) and Cas9, there was a third, critically important component: tracrRNA (trans-activating crRNA) . This was a small but crucial RNA molecule.pmc.ncbi.nlm.nih+1

This was a groundbreaking observation because the tracrRNA turned out to be a “bridge”—it connected Cas9 to the krRNA in such a way that Cas9 knew where to look and where to cut.pmc.ncbi.nlm.nih

2012: The Turning Point When Nature Became a Tool

Now Doudna and Charpentier had all the pieces of the puzzle. In their UC Berkeley/Umeå lab, they worked together (communicating across the ocean) to assemble CRISPR-Cas9 into something that could be a controllable tool.embryo.asu

Their key contribution was elegant: instead of using two separate RNA molecules (krRNA and tracrRNA), they combined them into a single molecule , which they called single guide RNA (sgRNA) .embryo.asu

Why was this important? Because it simplified the technology. Instead of programming two different RNAs, scientists now had to program just one. It was like going from using a computer with two buttons to one with a single large button labeled with what you wanted to do.mpg+1

Experiment: Testing in Dish

In their experiment, Doudna, Charpentier and their team (including Martin Jinek and Michael Hauer from Berkeley, and Krzysztof Chylinski and Ines Fonfara from Umeå) set up a laboratory scene:embryo.asu

They produced pure Cas9 protein – an enzyme not yet “programmed”embryo.asu
They created guide RNA that could program Cas9 to search for a specific DNA sequence.embryo.asu
They combined them in a laboratory tube – along with the target DNAembryo.asu

And they waited.

What happened: Cas9 precisely cut the DNA exactly where the guide RNA told it to . Not just anywhere—right there.embryo.asu

But that wasn’t the goal. Doudna and Charpentier were pursuing something much bigger: demonstrating that the CRISPR-Cas9 system can be programmed like a hyper-precise tool that scientists can target to ANY DNA sequence .embryo.asu

When Doudna and Charpentier showed they could program five different guide RNAs, each targeting a different site in the DNA, the idea was clear: It could work for any sequence a scientist wanted to edit .embryo.asu

Science Publication: The Moment When Everything Changed

Their manuscript reached the editorial office of Science in 2012.pmc.ncbi.nlm.nih

In the June 2013 issue of Science , an article was published: “RNA-guided genetic engineering of human pluripotent stem cells.” The title didn’t sound revolutionary, but its content was incredible.pmc.ncbi.nlm.nih

The article included a detailed description of the three CRISPR-Cas9 components:pmc.ncbi.nlm.nih

Cas9 protein (enzyme)
crRNA (lead part)
tracrRNA (connector)

And importantly , they showed how all three could work together as a programmed, precise DNA editing tool .pmc.ncbi.nlm.nih

But that was only part of it. Doudna and Charpentier proposed something radical: What if scientists could use this system not only in bacteria, but also in eukaryotic cells—like human cells?pmc.ncbi.nlm.nih

The scientific world reacted with madness.

The Year After: Feng Zhang and the First Editions in Mammalian Cells

In 2013, just a few months after Doudna-Charpentier’s publication, Feng Zhang of the MIT Broad Institute published his own paper in Science .embryo.asu

Zhang took the CRISPR-Cas9 described by Doudna and Charpentier and demonstrated that it could be delivered into living mouse and human cells and edit their genome .embryo.asu

It was a massively important demonstration. Theoretically, it worked in a tube. But would it work in living cells? Yes, and Zhang is proof.embryo.asu

Now scientists had not only a conceptual tool, but a practical tool.

Revolution: Six Months, Thousands of Articles

Six months after Doudna-Charpentier’s publication, dozens of labs around the world had already begun experimenting with CRISPR-Cas9.news.berkeley

Here’s why CRISPR was so transformative compared to previous technologies (such as ZFNs – Zinc Finger Nucleases, and TALENs – Transcription Activator-Like Effector Nucleases):ijisrt

aspect	ZFN	LANGUAGES	CRISPR-Cas9
Ease of design	Very difficult, requires protein engineering	Difficult, but easier than ZFN	Very easy – just change the RNA
Time to act	Weeks/months	Days/weeks	Hours/days
Cost	Dear	Easy	Very cheap
Precision	High	High	High
Versatility	Limited to certain sequences	More universal	Universal
Multiplex (multiple targets at once)	Difficult	Difficult	Easy

Scientists could now take any DNA sequence – from a human gene, mitochondrial DNA, bacteria, plants – and program Cas9 to cut it in hours.news.berkeley

It was like going from handwriting every letter of a document to having a golden pen that could write whatever you wanted.

First Triumphs: 2013-2015

By 2015, CRISPR-Cas9 had already been used to:

Gene editing in mouse cells – creating disease modelsaddgene
Mutation Repair – Scientists Worked on Serum Fibrosis and Beta-Thaliasiaaddgene
Gene function research – blocking genes to see what they doaddgene
Plant resistance formations – plants resistant to drought or diseaseaddgene

In 2015, Science named CRISPR its “Breakthrough of the Year” – the only laboratory tool to win this prestigious award.bitesizebio

Parallel History: The Battle for Patents

While Doudna and Charpentier published their results in Science , almost simultaneously, Zhang at MIT/Broad Institute was also working on the CRISPR project. The result: a patent controversy exists today.insights

Doudna and Charpentier filed their patent application in March 2013, but with priority from May 2012.insights

Zhang submitted his application in October 2013, but with priority from December 2012.insights

Zhang received the first patent – the U.S. Patent and Trademark Office granted him Patent No. 8,697,359 in April 2015. But Doudna and Charpentier also hold patents (European and other).broadinstitute+1

In the world of medicine and business – where patents mean money – this battle continues to this day.

A Dramatic Turning: The Nobel Prize in 2020

In a year when the world was grappling with COVID-19, the Swedish Academy of Sciences awarded the 2020 Nobel Prize in Chemistry to exactly two women: Emmanuelle Charpentier and Jennifer Doudna “for developing a method for genome editing.”Nobel Prize

This was historic. It was the first time the Nobel Prize in Chemistry was awarded solely to two women . Charpentier and Doudna were pioneers not only in science but also in gender equality in science.pmc.ncbi.nlm.nih

During her Nobel speech, Doudna expressed her gratitude to Charpentier: “Without her commitment and vision, this would not have been possible.”

From 2013 to 2025: How Far We’ve Come

Fast forward to today. Since the first Science article in 2012, CRISPR has gone from a laboratory curiosity to a real-world tool in medicine:

2019 : First CRISPR clinical trial in sickle cell patients in the USpmc.ncbi.nlm.nih
2023 : FDA approves the first CRISPR-Cas9-based drug for sickle cell disease and thalassemia – Casgevypmc.ncbi.nlm.nih
2024 : More than 1,500 CRISPR clinical trials worldwideinnovationhub
2025 : CRISPR-edited cells are now being delivered to patients who say they “feel like new people”innovationhub

Summary: How Bacteria Taught Us to Heal

The story of CRISPR is a story of discovery that began with curiosity—why do bacteria have these strange DNA repeats?—and led to a medical revolution.

From Yoshizumi Ishino in 1987 discovering the mysterious sequences, to Francisco Mojica understanding their function, to Jennifer Doudna and Emmanuelle Charpentier seeing that the bacterial immune system could be a tool for humanity – each step has been extraordinary.mdpi+4

What bacteria have developed over millions of years of evolution—a self-defense system against viruses—has taught us how to treat human genetic diseases. Nature is our best engineer. We just had to pay attention.pmc.ncbi.nlm.nih+1

Today, in 2025, CRISPR is beyond the “can work” stage and entering the “actually works in patients” stage. This journey from infectious discovery to reliable medical tool took 38 years. But the wait was worth it.

Sources and References

– MDPI: CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019)mdpi
– PMC/NIH: CRISPR-Cas9: From a bacterial immune system to genome-edited human cells in clinical trials (2017)pmc.ncbi.nlm.nih
– BioCompare: The History and Evolution of CRISPR (2021)biocompare
– Lab Biotechnology EU: Francis Mojica, the Spanish Scientist Who Discovered CRISPR (2022)labiotech
– Bitwise Bio: A Brief History of CRISPR-Cas9 Genome-Editing Tools (2024)bitesizebio–
Wikipedia: Francisco Mojicawikipedia
– Innovative Genomics Institute: Jennifer Doudna and Emmanuelle Charpentier – Behind the Development of CRISPR (2025)innovativegenomics
– Flagship Pioneering: A History of CRISPR (2020)flagshippioneering
– PMC/NIH: Nobel Prize 2020 in Chemistry honors CRISPR (2020)pmc.ncbi.nlm.nih
– PMC/NIH: Breaker of chains (2021)pmc.ncbi.nlm.nih
– ASU Embryo Project: Jennifer Doudna and Emmanuelle Charpentier’s Experiment (2017)embryo.asu
– Broad Institute: Statements and background on CRISPR patent process (2025)broadinstitute
– CRISPR Therapeutics: Dr. Emmanuelle Charpentiercrisprtx
– Insights.bio: Revolutionizing genome editing with CRISPR/Cas9: patent dispute (2015)insights
– Max Planck Institute: Emmanuelle Charpentier: An artist in gene editing (2017)mpg
– Nobel Prize Official: Jennifer A. Doudna (2018)Nobel Prize
– PMC/NIH: The genome-editing decade (2021)pmc.ncbi.nlm.nih
– PMC/NIH: Blossom of CRISPR technologies and applications (2018)pmc.ncbi.nlm.nih
– International Journal of Innovation and Scientific Research: Comparative Review of ZFN, TALEN, and CRISPR/Cas9ijisrt
– UC Berkeley News: How CRISPR worksnews.berkeley
– AddGene: CRISPR History and Development for Genome Engineering (2024)addgene
– Innovation Hub: The Breakthrough of CRISPR (2023ub: The Breakthrough of CRISPR (2023)pmc.ncbi.nlm.nih

标签： sgRNA

CRISPR: From Bacterial Defense System to Tool of the Future