The development and refinement of synthetic biology techniques have profoundly impacted our understanding of genetics and molecular biology. One of the most groundbreaking advances in this field is the construction of synthetic chromosomes using natural DNA components, a concept that was once relegated to the field of science fiction. Traditional methods for creating synthetic chromosomes have relied on de novo synthesis, which is inherently costly and time-consuming. This approach has limited the widespread adoption of chromosome synthesis in research and industry. However, the ability to build chromosomes using natural components presents an innovative and efficient alternative. The new method capitalizes on this concept, using segments of natural chromosomes and recombining them in a programmable manner. This technique aligns with the broader goals of synthetic biology, which include understanding complex biological systems and engineering them for various applications.
In a new study published in Nature Communications by Dr. Alessandro Coradini, Dr. Christopher Ne Ville, Dr. Zachary Krieger, Dr. Joshua Roemer, Dr. Cara Hull, Dr. Shawn Yang, Dr. Daniel Lusk & led by Professor Ian Ehrenreich from the University of Southern California, the researchers developed a novel method, CReATiNG (Cloning, Reprogramming, and Assembling Tiled Natural Genomic DNA), to construct synthetic chromosomes from natural DNA components in yeast. This approach represents a significant advancement in the field of synthetic biology.
The researchers identified specific segments from natural chromosomes of yeast. These segments were then excised from the chromosomes using CRISPR-Cas9 technology. CRISPR-Cas9 is a genome editing tool that allows for precise cutting of DNA at specified locations. After cutting, these natural chromosome segments were integrated into a cloning vector through a process known as homologous recombination. This step was crucial for manipulating and assembling these segments later on. The cloned segments were then co-transformed into recipient yeast cells. In these cells, the segments underwent programmable assembly into synthetic chromosomes. This was achieved through in vivo homologous recombination, a natural process in cells where similar or identical DNA strands exchange genetic material. The synthetic chromosomes assembled via CReATiNG were designed to replace the native chromosomes in the yeast cells. This demonstrated the functional viability of the synthetic chromosomes within a living organism. The researchers successfully used CReATiNG to synthetically recombine chromosomes between different yeast strains and species. This allowed them to study genetic variations and their phenotypic effects with high precision. The method was also applied to modify the structure of chromosomes. This involved rearranging the order of genes on the chromosomes, providing insights into how chromosome structure affects cell function and gene expression. They demonstrated the method’s capability for multiplex gene deletion by systematically eliminating non-essential genetic elements from the chromosome. This experiment showed the potential for streamlining chromosomes for specific functions or studies.
The new method is more efficient and less costly alternative to de novo chromosome synthesis. The method has vast applications in genetic research, biotechnology, and therapeutic development. Moreover, it opens up new avenues for understanding genetic diseases, gene functions, and the structural requirements of chromosomes. The ability to recombine and restructure chromosomes can lead to discoveries in genetic regulation, evolution, and synthetic biology. Coradini et al.’s work opens up a plethora of possibilities. One significant application is the exploration of genetic mechanisms underlying traits and diseases. By using CReATiNG to synthetically recombine chromosomes between strains and species, researchers can dissect the genetic basis of phenotypic differences with unprecedented precision. This could lead to breakthroughs in understanding complex genetic diseases and the development of targeted therapies. Another intriguing application is in the realm of chromosome restructuring. By modifying the arrangement of genes on chromosomes, scientists can probe the structural requirements of chromosomes and their impact on cellular functions. This could provide insights into chromosome evolution and the regulatory mechanisms governing gene expression. Moreover, the multiplex deletion capabilities of CReATiNG allow for the systematic elimination of non-essential genetic elements, streamlining chromosomes for various purposes. This could be particularly beneficial in industrial biotechnology, where streamlined organisms can be engineered for more efficient production of biofuels, pharmaceuticals, and other bioproducts.
While CReATiNG is a revolutionary technique, it is not without its challenges. The complexity of chromosome assembly increases with the number of segments involved, and unforeseen genetic interactions can arise. For instance, the unexpected discovery of SYN8’s essential role in a multiple deletion background highlights the intricate web of genetic interactions that exist within a cell. This underscores the need for comprehensive genetic analyses and cautious interpretation of results in synthetic biology experiments. The future of CReATiNG and similar methods lies in their refinement and broadening of applicability. Extending this technology to other organisms, including multicellular models, could have far-reaching implications in genetics and biotechnology. Additionally, integrating this approach with other synthetic biology tools, such as CRISPR-Cas systems, could further enhance its capabilities. In summary, Coradini et al.’s research provided a novel and efficient method for constructing synthetic chromosomes from natural components, greatly expanding the capabilities and applications of synthetic biology.
Coradini ALV, Ville CN, Krieger ZA, Roemer J, Hull C, Yang S, Lusk DT, Ehrenreich IM. Building synthetic chromosomes from natural DNA. Nat Commun. 2023 Dec 20;14(1):8337. doi: 10.1038/s41467-023-44112-2.