Cornell researchers from the Barstow Research Team have engineered a new strain of the bacteria Vibrio natriegens that increases its cloning ability and simplifies plasmid transformation, according to a study published on Feb. 13 in the Proceedings of the National Academy of Sciences Nexus.
A plasmid is a small, circular deoxyribonucleic acid that is separate from a cell’s chromosomal DNA. It is relevant in transformation — the process of taking in DNA from the environment. A competent cell possesses the ability to undergo transformation.
According to lead author and postdoctoral researcher at the Barstow Lab, David Specht Ph.D. ’21, V. natriegens is naturally competent in starvation conditions and in the presence of chitin — a sugar found in the shells of lobsters, crabs and shrimp.
The team enhanced the natural competency of this bacteria by engineering it to take in DNA even in the absence of chitin. The researchers plan to work towards eventually removing the competency requirement for starvation conditions.
The researchers found that their engineered strain could be grown, transformed and recovered without having to exchange the media — a gel or liquid containing nutrients for growth. This change simplifies the process of maintaining competency in the cell during potential disruptions like media exchange.
While natural competence usually occurs with similar DNA from related organisms, according to Specht, the ability of V. natriegens to take up plasmids is an important distinction.
“If you can [take up] plasmids, that means you can take any arbitrary piece of DNA and [the cell] will take it up. That’s technologically quite powerful,” Specht said.
According to co-author and lab manager Timothy Sheppard M.Eng. ’22, most experiments in synthetic biology — the science of engineering organisms — begin with the cloning of a gene into a cell and maintaining that DNA in subsequent copies. This is expensive as it requires equipment including a deep freezer, a still incubator, a shaking incubator and centrifuges.
A deep freezer maintains low temperatures needed to maintain cells and cultures. An incubator promotes the growth of cells by controlling environmental factors like temperature and humidity.
A still air incubator does not have a fan which leads to temperature variation within the levels of the incubator while a shaking incubator shakes the tubes, removing the need for a separate shaker. Centrifuges allow for molecules to be separated based on density by spinning the solution.
This is true for the bacteria Escherichia coli which is largely regarded as the chassis — a cellular host that holds engineered biological systems — of synthetic biology for its relative simplicity. While it is easy to produce, it requires the aforementioned tools that are costly and prevent large-scale accessibility.
For labs with low resources, both in terms of money for the equipment and the energy to maintain the equipment, V. natriegens eliminates this cost barrier as it will naturally take up DNA at room temperature and without a need to be shaken unlike with E. coli which is done to provide air and promote growth. V. natriegens also possesses a fast growth rate over E. coli.
This democratization offers greater possibilities for the advancement of synthetic biology through the expanded accessibility to low-resource labs and labs in other fields.
“A lot of places across the globe have very unequal access to synthetic biology, largely because of a lack of infrastructure and resources, but if we want to get anywhere with syn[thetic] bio at large, we all have to be on the same page,” Sheppard said. “We think that this could be a really great starting point.”
This also extends to education and even high schools. Competitions like the International Genetically Engineered Machine — which focuses on using synthetic biology to tackle various issues — are open to both high school students and undergraduates, but are often limited to wealthy high schools with the resources.
“To eliminate a bunch of the [capital equipment needed] for cloning makes synthetic biology more accessible and can really expand the reach of programs like iGEM so even schools with moderate resources could conceivably do this kind of stuff,” Specht said.
Specht also noted that due to the simplicity of the growth and transformation process, and lack of media exchange for V. natriegens, for things like protein production, it could be applied in new ways such as by robotizing the process to achieve large-scale cloning that has been difficult and expensive to do with E. coli.
However, while the team’s genetically engineered strain of V. natriegens can increase accessibility for low-resource labs, the question remains whether V. natriegens will replace E. coli in labs that are well-equipped and funded, especially in consideration of the copious amounts of existing research on E. coli.
Sheppard cautioned against ruling V. natriegens out because of the prominence of E. coli for the past 70-plus years. Rather, he encourages using research from E. coli to improve on V. natriegens and potentially surpass E. coli. In the field of synthetic biology where there is still a lot of potential, especially in light of increasing interest and concern over genetic modifications, V. natriegens offers a new, accessible alternative.
“I think it’s important for people who are dismissive of this due to decades of established E. coli practice to recognize that V. natriegens is a second option that can make things better and faster,” Sheppard said. “If we’re all a little more open to the possibilities of moving away from what we know, which I believe science should be, we could see some really incredible outcomes.”
Brenda Kim can be reached at [email protected].