Heralded as a breakthrough in synthetic biology, scientists in the US have created a type of bacteria with a manmade genome that is capable of self replicating: they designed the genome in a computer, synthesized it in the laboratory using chemicals and host organisms, then transplanted it into a recipient cell which then went on to self-replicate under the control of only the synthetic genome.
They suggest the new method could be used to explore the machinery of life and also engineer bacteria with a range of uses such as to produce biofuels, drugs and clean up the environment.
You can read about how the research team, led by Craig Venter of the J Craig Venter Institute, a not for profit genome research establishment with labs in in Rockville, Maryland and San Diego, California, achieved this “proof of principle” breakthrough in a 20 May online issue of Science.
In this study the researchers brought together two previous achievements where they chemically synthesized a bacterial genome and successfully transplanted the natural genome of one bacteria cell into another.
Although not strictly a fully synthetic cell, in that only the genome is manmade, lead researcher Dr J Craig Venter who has been working in this field for the last 15 years, told the press that:
“This is the first synthetic cell that’s been made, and we call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer.”
“This becomes a very powerful tool for trying to design what we want biology to do,” said Venter, adding that they already have a number of applications in mind, such as designing algae to capture CO2 and make new hydrocarbons for fuel, or to speed up vaccine production, make new food ingredients, or clean up water.
In the journal paper, Venter and colleagues describe how they designed, synthesized and assembled the Mycoplasma mycoides JCVI-syn1.0 genome, made of 1.08 million base pairs, and then transplanted it into a Mycoplasma capricolum recipient cell to make new Mycoplasma mycoides cells controlled only by the synthetic chromosome.
They wrote that the only DNA in the cells was the manmade DNA sequence, including “watermark” sequences and “other designed gene deletions and polymorphisms, and mutations acquired during the building process”. The watermark sequences were inserted so they could distinguish the synthetic cells from the wild ones.
To synthesize a genome with over a million base pairs, they had to use several steps, since current methods can only assemble short strips of DNA letters at a time.
First they inserted the shorter DNA sequences into yeast, where the organism’s repair enzymes knitted them together, then they transferred these medium sized strings into E. coli, then back into yeast, and so, until they had the full genome comprising over a million base pairs.
A J Craig Venter Institute statement described the process in more detail:
“The team designed 1,078 specific cassettes of DNA that were 1,080 base pairs long. These cassettes were designed so that the ends of each DNA cassette overlapped each of its neighbors by 80bp.”
Then, describing the three stages of the assembly process, they explain how they first took “10 cassettes of DNA at a time to build 110, 10,000 bp segments”, and in the second stage, took the “10,000 bp segments are taken 10 at a time to produce eleven, 100,000 bp segments”, and in the third and final stage, took “all 11, 100 kb segments were assembled into the complete synthetic genome in yeast cells and grown as a yeast artificial chromosome”.
They isolated the complete synthetic M. mycoides genome from the yeast cell and transplanted it into M. capricolum whose restriction enzymes had been removed. (Restriction enzymes “protect” a genome by cutting up DNA that does not belong to it, the process is thought to be a defence mechanism against pathogens like viruses that invade the DNA of host cells.)
The DNA from the synthetic genome was transcribed into messenger RNA (a key stage of gene expression, when the DNA instructions are turned into proteins that do the work in the organism) which were then translated into new proteins.
The researchers said the genome of the recipient cell, M. capricolum, was either destroyed by the restriction enzymes from M. mycoides, or was “lost during cell replication”.
After two days of culturing in a petri dish, viable cells of M. mycoides, which contained only synthetic DNA, were clearly visible, said the researchers.
Well aware of the social and ethical considerations of this type of science, the researchers requested a bioethical review early on in their investigations, back in the late 1990s.
“We have been consumed by this research, but we have also been equally focused on addressing the societal implications of what we believe will be one of the most powerful technologies and industrial drivers for societal good.”
“I think this is the first incidence in science where the extensive bioethical review took place before the experiments were done,” he told the press.
“It’s part of an ongoing process that we’ve been driving, trying to make sure that the science proceeds in an ethical fashion, that we’re being thoughtful about what we do and looking forward to the implications to the future,” he added.
Synthetic Genomics Inc, a company co-founded by Venter and his colleague Dr Hamilton O. Smith, funded the research.
“Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome.”
Daniel G. Gibson, John I. Glass, Carole Lartigue, Vladimir N. Noskov, Ray-Yuan Chuang, Mikkel A. Algire, Gwynedd A. Benders, Michael G. Montague, Li Ma, Monzia M. Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Lei Young, Zhi-Qing Qi, Thomas H. Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Hutchison, III, Hamilton O. Smith, and J. Craig Venter.
Sources: American Association for the Advancement of Science, J Craig Venter Institute.
Written by: Catharine Paddock, PhD