Life’s genetic code has only ever contained four natural bases. These bases pair up to form two “base pairs”—the rungs of the DNA ladder—and they have simply been rearranged to create bacteria and butterflies, penguins and people. Four bases make up all life as we know it.
Until now. Scientists at The Scripps Research Institute (TSRI) have announced the development of the first stable semisynthetic organism. Building on their 2014 study in which they synthesized a DNA base pair, the researchers created a new bacterium that uses the four natural bases (called A, T, C and G), which every living organism possesses, but that also holds as a pair two synthetic bases called X and Y in its genetic code.
TSRI Professor Floyd Romesberg and his colleagues have now shown that their single-celled organism can hold on indefinitely to the synthetic base pair as it divides. Their research was published January 23, 2017, online ahead of print in the journal Proceedings of the National Academy of Sciences.
“We’ve made this semisynthetic organism more life-like,” said Romesberg, senior author of the new study.
While applications for this kind of organism are still far in the future, the researchers say the work could be used to create new functions for single-celled organisms that play important roles in drug discovery and much more.
Building a Unique Organism
When Romesberg and his colleagues announced the development of X and Y in 2014, they also showed that modified E. coli bacteria could hold this synthetic base pair in their genetic code. What these E. coli couldn’t do, however, was keep the base pair in their code indefinitely as they divided. The X and Y base pair was dropped over time, limiting the ways the organism could use the additional information possessed in their DNA.
“Your genome isn’t just stable for a day,” said Romesberg. “Your genome has to be stable for the scale of your lifetime. If the semisynthetic organism is going to really be an organism, it has to be able to stably maintain that information.”
Romesberg compared this flawed organism to an infant. It had some learning to do before it was ready for real life.
In stepped TSRI Graduate Student Yorke Zhang and Brian Lamb, an American Cancer Society postdoctoral fellow in the Romesberg lab at the time of the study. Together, they helped develop the means for the single-celled organism to retain the artificial base pair.
First, Zhang and Lamb, co-first authors of the study, optimized a tool called a nucleotide transporter, which brings the materials necessary for the unnatural base pair to be copied across the cell membrane. “The transporter was used in the 2014 study, but it made the semisynthetic organism very sick,” Zhang explained. The researchers discovered a modification to the transporter that alleviated this problem, making it much easier for the organism to grow and divide while holding on to X and Y.
Next, the researchers optimized their previous version of Y. The new Y was a chemically different molecule that could be better recognized by the enzymes that synthesize DNA molecules during DNA replication. This made it easier for cells to copy the synthetic base pair.
A New Use for CRISPR-Cas9
Finally, the researchers set up a “spell check” system for the organism using CRISPR-Cas9, an increasingly popular tool in human genome editing experiments. But instead of editing a genome, the researchers took advantage of CRISPR-Cas9’s original role in bacteria.
The genetic tools in CRISPR-Cas9 (a DNA segment and an enzyme) originated in bacteria as a kind of immune response. When a bacterium encounters a threat, like a virus, it takes fragments of the invader genome and pastes them into its own genome—a bit like posting a “wanted” poster on the off chance it sees the invader again. Later, it can use those pasted genes to direct an enzyme to attack if the invader returns.
Knowing this, the researchers designed their organism to see a genetic sequence without X and Y as a foreign invader. A cell that dropped X and Y would be marked for destruction, leaving the scientists with an organism that could hold on to the new bases. It was like the organism was immune to unnatural base pair loss.
“We were able to address the problem at a fundamental level,” said Lamb, who now serves as a research scientist at Vertex Pharmaceuticals.
Their semisynthetic organism was thus able to keep X and Y in its genome after dividing 60 times, leading the researchers to believe it can hold on to the base pair indefinitely.
“We can now get the light of life to stay on,” said Romesberg. “That suggests that all of life’s processes can be subject to manipulation.”
A Foundation for Future Research
Romesberg emphasized that this work is only in single cells and is not meant to be used in more complex organisms. He added that the actual applications for this semisynthetic organism are “zero” at this point. So far, scientists can only get the organism to store genetic information.
Next, the researchers plan to study how their new genetic code can be transcribed into RNA, the molecule in cells needed to translate DNA into proteins. “This study lays the foundation for what we want to do going forward,” said Zhang.
Headquartered in San Diego, California with a sister facility in Jupiter, Florida, the institute is home to 3,000 scientists, technicians, graduate students, and administrative and other staff, making it among the largest private, non-profit biomedical research organizations in the world.
TSRI’s California campus is located on 35 acres (140,000 m2) of land between the Torrey Pines State Reserve and the University of California, San Diego in La Jolla. In Florida, TSRI occupies 30 acres (120,000 m2) adjacent to the John D. MacArthur campus of Florida Atlantic University in Palm Beach County, Florida.
The Florida campus of TSRI operates a 350,000-square-foot (33,000 m2) state-of-the-art biomedical research facility focusing on neuroscience, cancer biology, medicinal chemistry, drug discovery, biotechnology, and alternative energy development. Approximately 450 faculty, staff and students occupy TSRI’s Florida campus. TSRI Florida is housed on the Jupiter campus of Florida Atlantic University.
The Scripps Research Institute research articles from Innovation Toronto
- New Method Enlists Electricity for Easier, Cheaper, Safer Chemistry – May 11, 2016
- A Cheap, Portable Drug-Discovery System: LIGHTSABR – February 14, 2016
- Scripps Florida Scientists Reveal Potential Treatment for Life-Threatening Viral Infections – November 25, 2015
- Cancer Treatment Breakthrough: Researchers Engineer A Way To Make Leukemia Cells Kill Each Other – October 23, 2015
- Progress towards a universal, and perhaps, lifelong flu vaccine – August 30, 2015
- Scripps Research, Mayo Clinic Scientists Find New Class of Drugs that Dramatically Increases Healthy Lifespan – March 10, 2015
- Scientists Announce Anti-HIV Agent So Powerful It Can Work in a Vaccine – February 19, 2015
- Scientists Open New Frontier of Vast Chemical ‘Space’ – December 21, 2014
- Scripps Florida Scientists Make Diseased Cells Synthesize Their Own Drug – September 6, 2014
- Scripps Research Institute Chemists Uncover Powerful New Click Chemistry Reactivity – August 18, 2014
- Scientists Add Letters to DNA’s Alphabet, Raising Hope and Fear | synthetic biology – May 8, 2014
- Scripps Research Institute Scientists Create First Living Organism that Transmits Added Letters in DNA ‘Alphabet’ | DNA biology – May 7, 2014
- Scientists find new way to upgrade natural gas
- Scripps Research Institute Scientists Identify First Potentially Effective Therapy for Human Prion Disease
- Innovative Screening Strategy Swiftly Uncovers New Drug Candidates, New Biology | drug-discovery strategy
- Clinical Trial Indicates Gabapentin Is Safe and Effective for Treating Alcohol Dependence
- New Strategy to Treat Multiple Sclerosis Shows Promise in Mice
- Scripps Florida Scientists Identify Potential New Drug for Inherited Cancer
- Drug Candidate Leads to Improved Endurance
- New Drug Candidate Has Dramatic Effect on Endurance
- New Compound Excels at Killing Persistent and Drug-Resistant Tuberculosis
- Chemists Invent Powerful Toolkit, Accelerating Creation of Potential New Drugs
- Meth Vaccine Shows Promising Results in Early Tests
- New ‘Biopsy in a Blood Test’ to Detect Cancer
- Discovery May Lead to Safer Treatments for Asthma, Allergies and Arthritis
- First Stem Cells from Endangered Species
- Can a vaccine stop drug abuse?
- Addicted to Fat: Overeating May Alter the Brain as Much as Hard Drugs
There are lessons to be learned from venoms.
Scorpions, snakes, snails, frogs and other creatures are thought to produce tens or even hundreds of millions of distinct venoms. These venoms have been honed to strike specific targets in the body.
For victims of a scorpion’s sting, that spells doom. For scientists, however, the potent molecules in venoms hold the potential to be adapted into medicines. But venoms are difficult to isolate and analyze using traditional methods, so only a handful have been turned into drugs.
Now a team led by scientists at The Scripps Research Institute (TSRI) has invented a method for rapidly identifying venoms that strike a specific target in the body—and optimizing such venoms for therapeutic use.
The researchers demonstrated the new method by using it to identify venoms that block a certain protein on T cells—a protein implicated in multiple sclerosis, rheumatoid arthritis and other inflammatory disorders. The researchers then used their method to find an optimized, long-acting variant of a venom that blocks this protein and showed that the new molecule powerfully reduces inflammation in mice.
“Until now we haven’t had a way to seriously harness venoms’ vast therapeutic potential,” said principal investigator Richard A. Lerner, Lita Annenberg Hazen Professor of Immunochemistry at TSRI.
The report on the advance by Lerner and his colleagues was selected as a “Hot Paper” and cover story by the journal Angewandte Chemie.
Choose Your Poison
The use of venoms as therapies may seem paradoxical, since these molecules generally evolved to harm and kill other organisms. But a low dose delivered to the right place can sometimes have highly beneficial effects. The pain-killing drug ziconotide (Prialt®), for example, is derived from one of the venoms used by cone-snails to immobilize their fishy prey. Venoms also are attractive from a drug development perspective because they tend to hit their targets on cells with very high potency and selectivity.
Carbon-Carbon Coupling Made Easy
Scientists at The Scripps Research Institute (TSRI) have devised a new molecule-building method that is likely to have a major impact on the pharmaceutical industry and many other chemistry-based enterprises.
The method, published as an online First Release paper in Science on April 21, 2016, allows chemists to construct novel, complex and potentially very valuable molecules, starting from a large class of compounds known as carboxylic acids, which are relatively cheap and non-toxic. Carboxylic acids include the amino acids that make proteins, fatty acids found in animals and plants, citric acid, acetic acid (vinegar) and many other substances that are already produced in industrial quantities.
“This is one of the most useful methods we have ever worked with, and it mostly involves materials that every chemist has access to already, so I think the interest in it will expand rapidly,” said principal investigator Phil S. Baran, Darlene Shiley Professor of Chemistry at TSRI.
“This exciting new discovery represents a significant advance in our ability to transform simple organic molecules and to rapidly build complex structures from readily available materials—we expect to use it in both the discovery and development of biologically active compounds that help patients prevail over serious disease,” said co-author Martin D. Eastgate, a Director in Chemical and Synthetic Development at Bristol-Myers Squibb, who participated in the study as part of a long-standing research collaboration between Bristol-Myers Squibb and TSRI.
A new study led by scientists at The Scripps Research Institute (TSRI) reveals a previously unknown type of immune cell. The discovery opens new avenues in the effort to develop novel therapies for autoimmune diseases such as type 1 diabetes.
The newly discovered cells resemble conventional T cells, yet are biased toward becoming T regulatory cells (Tregs), which protect the body from autoimmune disease.
“This study was eye-opening,” said study senior author and TSRI biologist Oktay Kirak. “You wouldn’t expect these cells to have this ability. The best analogy I have is Clark Kent turning into Superman. Clark Kent looks like an Average Joe, so no one would expect him to have the same abilities as Superman.”
Stopping Type 1 Diabetes
The body has an army of millions of immune cells. These cells contain receptors generated through random genetic rearrangements–a clever strategy to keep them ready to fight unfamiliar viruses and bacteria. This diverse pool leaves many questions for scientists, however, about which ones are active in specific diseases.
One puzzling disease is type 1 diabetes, in which immune cells mistakenly attack insulin-producing cells in the pancreas. Scientists know that Tregs should be able control this autoimmune response, deflecting the attack. Current clinical trials are focusing on increasing the numbers of Treg cells and finding ways to make them enter the pancreas.
In the new study, researchers began to solve this problem by isolating an individual Treg from a mouse model of type 1 diabetes and inserting its nucleus–which contained the unique genetic immune receptor information–into a mouse egg cell that had its own nucleus removed.
Using this cloning method (Somatic Cell Nuclear Transfer), the scientists created a mouse model that produced only the original Treg, allowing them to study its origins and functions for the first time.