Humans, like computers, are programmed. Our lifeblood is encoded in our DNA, a long helix of nucleic acids that contains our instructions. Combinations of four letters (A, C, G, and T) that give rise not only to us but to all the different organisms with one thing in common: life.
Great progress has been made to understand the molecular basis of life since the discovery of DNA in the 1950s. We know how to read, edit, and engineer this molecule, but still we don’t fully understand all its information. Do living organisms really need all the genetic content that they have? Are all the genes functional, and do they all play a role in keeping us alive? If not, which part of the genetic material is essential for an organism to be alive?
To answer these basic questions of biology, our partners from the University of Göttingen, Jörg Stülke and Fabian Commichau, work with some of the first existing forms of life: bacteria. These microorganisms are unicellular and have small and simple genomes, which makes them a perfect model to unravel our basic questions of life.
In their approach, Stülke and Commichau aim to find the essential genes of the bacterium Bacillus subtilis by eliminating all those that seem unnecessary and define a so-called Mini-Bacillus: “with reducing the genome we can try to find out what is really required to keep a living organism running, which functions are required for life, what is life, essentially”, comments Stülke.
with reducing the genome we can try to find out what is really required to keep a living organism running, which functions are required for life, what is life, essentially”
They started by removing large and non-essential parts of the genome and check afterwards if the minimal strains that they produce are viable and stable. In approximately three and a half years of work, they have reduced the genome of this organisms by approximately 40%, which is the highest reduction achieved on a complex bacterium so far. But they have only “harvested the low hanging fruits”, says Stülke, and they estimate that it will be a very time-consuming process to remove all the remaining non-essential regions: it could take five to ten more years to reach the minimal genome that they have predicted.
In contrast to other approaches that aim at engineering an organism by putting together individual genes, reducing the genome of an existing microorganism is not only useful to understand the essential genes for life, but also to discover unexpected functions that have been overseen. For example, Commichau talks about how following the top-down approach in B. subtillis led to the discovery of previously unknown genes responsible for its capacity to uptake DNA without any special treatment, which is a very important feature that highly facilitates the engineering of this organism.
Although the results of these investigations depend on the experimental settings and are not easy to extrapolate to other organisms, some general conclusions can be drawn already. Stülke remarks: “Here is one thing that we already now can learn from this, and this applies to Bacillus via yeast and worm to man. That we have functions that were so far underestimated”. While it is clear for all how basic elements like a functional cell membrane or the DNA replication machinery [the one in charge of copying our genetic material in cell division] are key for life, Stülke highlights how there are many functions that “people didn’t think of and we know now they are really important and we need them in a minimal cell”. Among these functions he highlights the role of protective enzymes, such as those involved in the detoxification of toxic metabolites that are generated as by-products of the normal metabolisms and that need to be cleared out of the cell to maintain its function.
In addition to the many answers that the Mini-Bacillus can provide to understand the basis of life, such mini-bacterium can become a great tool for biotechnology purposes. For our project Rafts4Biotech, a microbe bearing a minimal genome is conceived like a perfect chassis that researchers can customise to fulfil their production requirements. As Commichau explains: “We can bring back some genes [into the Mini-Bacillus] and have a tailor-made organism for any desired reaction”. In addition to the versatility that such a microbial chassis offers, Commichau emphasises how using a bacterium with a reduced genome, the interferences between the metabolic reactions of the microbe and the introduced reactions with an industrial interest can be lowered, highly improving the production yields.
We can bring back some genes and have a tailor-made organism for any desired reaction”
The Mini-Bacillus project is a great example that shows how tackling some of the most fundamental questions of biology can both provide valuable answers for understanding the basis of life, while simultaneously translating into applied solutions that fulfil our current social needs with biotechnology.