The accelerated evolution engine known as T7-ORACLE has revolutionized the field of medicine and biotechnology by allowing researchers to evolve proteins with new or improved functions at an unprecedented rate. This breakthrough was achieved by Scripps Research scientists who have developed a synthetic biology platform that enables continuous evolution inside cells without damaging the cell’s genome.

Directed evolution is a laboratory process where mutations are introduced, and variants with improved function are selected over multiple cycles. Traditional methods require labor-intensive steps and can take weeks or more to complete. In contrast, T7-ORACLE accelerates this process by enabling simultaneous mutation and selection with each round of cell division, making it possible to evolve proteins continuously and precisely inside cells.

T7-ORACLE circumvents the bottlenecks associated with traditional approaches by engineering E. coli bacteria to host a second, artificial DNA replication system derived from bacteriophage T7. This allows for continuous hypermutation and accelerated evolution of biomacromolecules, making it possible to evolve proteins in days instead of months.

To demonstrate the power of T7-ORACLE, researchers inserted a common antibiotic resistance gene into the system and exposed E. coli cells to escalating doses of various antibiotics. In less than a week, the system evolved versions of the enzyme that could resist antibiotic levels up to 5,000 times higher than the original.

The broader potential of T7-ORACLE lies in its adaptability as a platform for protein engineering. Scientists can insert genes from humans, viruses, or other sources into plasmids and introduce them into E. coli cells, which are then mutated by T7-ORACLE to generate variant proteins that can be screened or selected for improved function.

This could help scientists more rapidly evolve antibodies to target specific cancers, evolve more effective therapeutic enzymes, and design proteases that target proteins involved in cancer and neurodegenerative disease. The system’s ease of implementation, combined with its scalability, makes it a valuable tool for advancing synthetic biology.

The research team is currently focused on evolving human-derived enzymes for therapeutic use and tailoring proteases to recognize specific cancer-related protein sequences. In the future, they aim to explore the possibility of evolving polymerases that can replicate entirely unnatural nucleic acids, opening up possibilities in synthetic genomics.

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Nature’s Armor: Scientists Uncover Gene Behind Aussie Skinks’ Immunity to Deadly Snake Venom

In a groundbreaking study led by the University of Queensland, scientists have discovered the genetic secret behind Australian skinks’ remarkable ability to withstand deadly snake venom. The research, published in the International Journal of Molecular Sciences, reveals that these small lizards have evolved a molecular armor to protect themselves from the toxic effects of neurotoxins.

Professor Bryan Fry from UQ’s School of the Environment explained that the skinks’ defense mechanism involves tiny changes in a critical muscle receptor called the nicotinic acetylcholine receptor. This receptor is normally targeted by snake venom, which blocks nerve-muscle communication and leads to rapid paralysis and death. However, in a stunning example of evolutionary adaptation, researchers found that skinks independently developed mutations on 25 occasions to block venom from attaching.

“It’s a testament to the massive evolutionary pressure exerted by venomous snakes after their arrival and spread across the Australian continent,” Professor Fry said. “The same mutations evolved in other animals like mongooses, which feed on cobras.”

Researchers confirmed that Australia’s Major Skink (Bellatorias frerei) has developed exactly the same resistance mutation as the honey badger, famous for its immunity to cobra venom.

To validate these findings, scientists conducted functional testing at UQ’s Adaptive Biotoxicology Laboratory. Dr. Uthpala Chandrasekara led the laboratory work and reported that the data was “crystal clear.” The modified receptors simply didn’t respond to toxins, demonstrating their remarkable ability to repel deadly snake venom.

This research has significant implications for biomedical innovation, particularly in the development of novel antivenoms or therapeutic agents. Dr. Chandrasekara emphasized that understanding how nature neutralizes venom can provide valuable clues for designing more effective treatments.

The project involved collaborations with museums across Australia and offers a promising example of interdisciplinary research, bridging the gap between scientific discovery and potential applications.

The field of genetic engineering has taken a significant leap forward with the development of two new genome editing technologies by a team of Chinese researchers led by Prof. Gao Caixia from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences. These innovations, collectively known as Programmable Chromosome Engineering (PCE) systems, have been published in the prestigious journal Cell.

The PCE system is an upgrade to the well-known Cre-Lox technology, which has long been used for precise chromosomal manipulation. However, this older method had three major limitations that hindered its broader application: low recombination efficiency, reversible recombination activity, and the need for a scar (a small DNA fragment) at the editing site.

The research team tackled each of these challenges by developing novel methods to advance the state of this technology. Firstly, they created a high-throughput platform for rapid recombination site modification and proposed an asymmetric Lox site design that reduces reversible recombination activity by over 10-fold.

Secondly, they utilized their recently developed AiCE model – a protein-directed evolution system integrating general inverse folding models with structural and evolutionary constraints – to develop AiCErec. This approach enabled precise optimization of Cre’s multimerization interface, resulting in an engineered variant with a recombination efficiency 3.5 times that of the wild-type Cre.

Lastly, they designed and refined a scarless editing strategy for recombinases by harnessing the high editing efficiency of prime editors to develop Re-pegRNA, a method that uses specifically designed pegRNAs to perform re-prime editing on residual Lox sites, precisely replacing them with the original genomic sequence.

The integration of these three innovations led to the creation of two programmable platforms, PCE and RePCE. These platforms allow flexible programming of insertion positions and orientations for different Lox sites, enabling precise, scarless manipulation of DNA fragments ranging from kilobase to megabase scale in both plant and animal cells.

Key achievements include targeted integration of large DNA fragments up to 18.8 kb, complete replacement of 5-kb DNA sequences, chromosomal inversions spanning 12 Mb, chromosomal deletions of 4 Mb, and whole-chromosome translocations. As a proof of concept, the researchers used this technology to create herbicide-resistant rice germplasm with a 315-kb precise inversion.

This groundbreaking work not only overcomes the historical limitations of the Cre-Lox system but also opens new avenues for precise genome engineering in various organisms, demonstrating its transformative potential for genetic engineering and crop improvement.