Question

Describe how the team from the J. Craig Venter Institute created a synthetic genome. How did the team demonstrate that the genome converted the recipient strain of bacteria into a different strain?

Short answer

Answer: The key steps involved in creating a synthetic genome and demonstrating its ability to convert a recipient strain of bacteria into a different strain include: 1) Creating a synthetic genome using synthetic genomics, 2) Assembling the synthetic genome inside a yeast cell, 3) Transferring the synthetic genome to a recipient bacterium, 4) Genome conversion, and 5) Demonstrating the conversion through protein analysis, morphological differences, and DNA sequencing.

Step-by-step solution

Creating a synthetic genome

The team from the J. Craig Venter Institute created a synthetic genome using a technique called "synthetic genomics." They designed a new DNA sequence, composed of smaller pieces of DNA called "oligonucleotides," which are assembled into the full genome sequence in a stepwise manner. They used the genome of an existing bacterium, Mycoplasma mycoides, as a reference and modified it according to their needs. The resulting synthetic genome was named Mycoplasma mycoides JCVI-syn1.0.

Assembling the synthetic genome

The team assembled the synthetic genome inside a yeast cell. They transferred the designed DNA sequence into the yeast cell, which then replicated the DNA and assembled it into a complete and functional chromosome. The yeast cell acted as a "factory" to produce copies of the synthetic genome.

Transferring the synthetic genome to a recipient bacterium

Once the synthetic genome was assembled, the team needed to transfer it into a living bacterium to study its effects. They chose Mycoplasma capricolum as the recipient bacterium. To do this, they extracted the synthetic genome from the yeast cell and introduced it into the recipient bacterium using a technique called "electroporation," in which an electrical field is used to create small pores in the bacterial cell membrane, allowing the DNA to enter the cell.

Genome conversion

Once inside the recipient bacterium, the synthetic genome took control of the cell's machinery and began producing proteins based on the information stored in its DNA sequence. This effectively converted the recipient strain of bacteria (Mycoplasma capricolum) into the synthetically designed strain (Mycoplasma mycoides JCVI-syn1.0).

Demonstrating the conversion

To demonstrate that the genome conversion had occurred, the team performed several experiments. First, they analyzed the proteins produced by the bacteria and found that they matched those expected from the synthetic genome. Additionally, they observed distinct morphological differences between the original recipient strain and the converted strain – the converted bacteria had a characteristic appearance of Mycoplasma mycoides. Lastly, they performed DNA sequencing to confirm that the bacteria carried the synthetic genome. By following these steps, the team from the J. Craig Venter Institute successfully created a synthetic genome and demonstrated its ability to convert a recipient strain of bacteria into a different strain.

Key concepts

Synthetic Genomics

Synthetic genomics is an extraordinary field where scientists engineer new genomes or modify existing ones to create organisms with desired traits. In essence, it's like writing a book, but the letters are the building blocks of DNA, known as nucleotides. Using synthetic genomics, the team at the J. Craig Venter Institute developed a new genomic sequence by piecing together short DNA fragments called oligonucleotides.

They used the pre-existing Mycoplasma mycoides genome as a template and modified it to meet specific goals. Imagine a recipe that you fine-tune to your taste; similarly, the scientists adjusted the genome for desired characteristics, resulting in the synthetic Mycoplasma mycoides JCVI-syn1.0 genome.

Genome Assembly

Imagine trying to solve a giant jigsaw puzzle; that's what genome assembly is like but at a molecular level. To put together the synthetic genome, the researchers utilized a yeast cell as a natural factory for DNA processing. They inserted the designed DNA fragments into the yeast, which acted as an assembly line, replicating and stitching the pieces into a fully functional chromosome.

This ingenious use of yeast simplified the complex process of genome assembly, bridging the gap between a digital genetic code and a physical DNA strand that could direct an organism's biological activities.

Electroporation

Electroporation might sound like something out of a science fiction movie, but it's a standard technique used in molecular biology. Think of it as 'door-opening' for cells. When scientists inserted the new synthetic genome into the recipient bacterium, they used this method to create tiny pores in the bacterium's membrane. How? By exposing the cells to a brief electrical pulse, which jolts the membrane just enough to let the DNA slip into the cell's interior.

It's a delicate balance – too little electricity and the DNA can't get in; too much, and the cell could be damaged. With the right parameters, electroporation is an efficient way to introduce new genetic material into cells, setting the stage for genomic conversion.

Genomic Conversion

Genomic conversion is akin to a software update on your computer, except this 'update' occurs at a biological level. After the synthetic genome was introduced into Mycoplasma capricolum through electroporation, it began to 'boot up' and take over the cell's operations. This essentially transformed the identity of the bacteria, similar to installing a new operating system that reprograms the hardware.

With the newly installed synthetic genome in place, the recipient bacteria stopped producing its original proteins and started making new proteins as dictated by the synthetic sequence. The conversion was complete: a bacterium now functioned according to the synthetic genome, representing a breakthrough in synthetic biology.

DNA Sequencing

To confirm that the new operating system – the synthetic genome – was successfully running in the bacteria, the scientists turned to DNA sequencing. This process is like double-checking that every line of code is correct after installing new software. By sequencing the DNA within the transformed bacteria, they could verify that the synthetic genome was present and correct.

Moreover, DNA sequencing allowed the scientists to ensure that no unwanted mutations had occurred during the assembly or insertion processes. It was the ultimate quality check, securing not only the success of this experiment but also reinforcing confidence in our ability to read and rewrite the code of life.