On March 28th, 2016 we learned about

Bacterium DNA crafted to avoid all possible complexities

The world has a new species of bacterium that possesses one big ability— to stay alive. This might not seem like a big deal compared to the multitudes of other organisms on Earth that have more or less mastered that particular feat, until you consider that this bacterium wasn’t shaped by millions of years of evolution, but designed by humans in a laboratory. What’s more, the fact that this species, called syn3.0, does so little is considered a big success, because the goal of the project was to make the most simplistic, minimal creature possible, hopefully exposing what life’s minimal specifications really are. Despite the custom design, that goal remains to be seen.

Avoiding a deluge of details

Bacteria are considered relatively simple life forms, as their cells lack many of the specialized structures found in the cells of eukaryotes like plants, fungi and animals. They usually carry less DNA as well, with only 4,000 to 5,000 genes, compared to the 22,000 found in humans. Even then, that number of genes represents a huge number of moving parts when you’re trying to understand the role of a single snippet of DNA at a time. Further complicating things is the fact that many genes function differently depending on what other genes are active in an organism— a biological process involving two genes can sometimes be carried out when one has failed, but not two, making isolating cause and effects very difficult. Some researchers have tried to unwind bacterial gene pools, removing gene at a time to see what changes, but a team at the J. Craig Venter Institute started from the bottom up, building syn3.0 nearly from scratch to end up with an organism surviving with a mere 473 genes.

Isolating the essential ingredients

Syn3.0’s genome was based on a blueprint offered by Mycoplasma mycoides, a bacterium that had been stripped down to 901 genes. The working recipe contains 195 genes for expressing DNA as functional RNA and proteins, 34 genes to control replication of the genome (ie, reproduction), 84 genes to regulate the actual cell structure, 81% for actual metabolic activity like eating, and 149 genes for… unknown purposes. Despite all the work to create a minimally viable cell, researchers found that some of the genes they’d omitted because they served no clear purpose were actually critical to the organism’s survival. There are guesses about around half of these mystery genes, but 79 genes’ functions are still completely opaque.

The goal of all this was to establish a baseline for life, and then use it build our understanding of more complex DNA from other organisms. The unknown genes complicate things, but they don’t completely negate the gains of this project, which should let researchers more easily isolate the effects of new genes that could be introduced a la carte to syn3.0’s genome. Obviously, work will continue to find out what is happening in the secret sauce of unknown genes, and further attempts to streamline the genome may be possible. Syn3.0 depends on being injected into the hollowed-out shell of another bacterium to get started, and even simpler organisms might be possible if you let them exist as symbionts inside a host cell. Of course, too much interdependancy risks introducing new variables to research, so for now syn3.0 represents a very functional shot at keeping things simple.


My first grader asked: So they started with a pile of genes and threw away the garbage parts?

The unused portions of more complex genomes wasn’t necessarily garbage, they just weren’t essential. Imagine building a car from scratch and considering the windshield— they’re very useful, but you could feasibly drive yourself from point A to point B without one, so it could be omitted.

 

Source: Scientists build minimum-genome bacterium by Tina Hesman Saey, Science News

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