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.

A team of researchers from UC Merced has made a groundbreaking discovery by creating tiny artificial cells that can accurately keep time, mimicking the daily rhythms found in living organisms. This achievement sheds light on how biological clocks stay on schedule despite the inherent molecular noise inside cells.

The study, published in Nature Communications, was led by bioengineering Professor Anand Bala Subramaniam and chemistry and biochemistry Professor Andy LiWang. The team’s findings show that artificial cells can glow in a regular 24-hour rhythm for at least four days when loaded with core clock proteins, one of which is tagged with a fluorescent marker.

However, when the number of clock proteins is reduced or the vesicles are made smaller, the rhythmic glow stops. This loss of rhythm follows a reproducible pattern, indicating that clocks become more robust with higher concentrations of clock proteins, allowing thousands of vesicles to keep time reliably – even when protein amounts vary slightly between vesicles.

To explain these findings, the team built a computational model that revealed another component of the natural circadian system – responsible for turning genes on and off – does not play a major role in maintaining individual clocks but is essential for synchronizing clock timing across a population. The researchers also noted that some clock proteins tend to stick to the walls of the vesicles, meaning a high total protein count is necessary to maintain proper function.

“This study shows that we can dissect and understand the core principles of biological timekeeping using simplified, synthetic systems,” Subramaniam said.

The work led by Subramaniam and LiWang advances the methodology for studying biological clocks, according to Mingxu Fang, a microbiology professor at Ohio State University and an expert in circadian clocks. “This new study introduces a method to observe reconstituted clock reactions within size-adjustable vesicles that mimic cellular dimensions,” Fang said. “This powerful tool enables direct testing of how and why organisms with different cell sizes may adopt distinct timing strategies, thereby deepening our understanding of biological timekeeping mechanisms across life forms.”

The study was supported by Subramaniam’s National Science Foundation CAREER award from the Division of Materials Research and by grants from the National Institutes of Health and Army Research Office awarded to LiWang.

The study published in Angewandte Chemie sheds light on how ribose may have become the preferred sugar for RNA development, highlighting its unique ability to bind with phosphate more quickly and effectively than other sugar molecules. This characteristic could have played a crucial role in selecting ribose as the building block of life.

Ramanarayanan Krishnamurthy, professor of chemistry at Scripps Research, emphasizes that this finding supports the idea that prebiotic chemistry could have produced the fundamental components of RNA, which eventually led to entities exhibiting lifelike properties. The research focuses on phosphorylation, a step within nucleotide-building where ribose connects to the phosphate group, and explores whether other sugars can undergo similar reactions.

The team’s experiments showed that while diamidophosphate (DAP) could phosphorylate all four sugar molecules tested, it phosphorylated ribose at a significantly faster rate. The reaction with ribose produced exclusively ring-shaped structures with five corners, whereas the other sugars formed a combination of 5- and 6-member rings.

“This really showed us that there is a difference between ribose and the three other sugars,” says Krishnamurthy. “Ribose not only reacts faster than the other sugars, it’s also more selective for the five-member ring form, which happens to be the form that we see in RNA and DNA today.”

When DAP was added to a solution containing equal amounts of the four different sugars, it preferentially phosphorylated ribose. The researchers demonstrated that this selective process produces a molecule with a form conducive for making RNA, providing further evidence for ribose’s preeminence.

While the study does not claim that these reactions directly led to life, it suggests that they might have played a crucial role in the primordial process that gave rise to the fundamental components of life. The researchers caution against over-interpretation and emphasize the need for further investigation into the emergence of life on Earth.

In future research, the team plans to test whether this chemical reaction can occur inside primitive cellular structures called protocells. If successful, it might provide a compelling explanation for how ribose became the preferred sugar for RNA development and ultimately gave rise to life as we know it today.