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Genes: How few needed for life?
What are the fewest genes needed to sustain life? To test that, scientists started with a
microbe having one of the smallest known genomes — or entire sets of genetic
instructions. Then scientists figured out the magic minimum for this microbe, which was
473 genes. By whittling down the genes to this number, scientists learned a lot about
biology. But there is still much to discover. Researchers still aren’t sure exactly what
almost a third of its genes do.
The new microbe is a stripped-down version of Mycoplasma mycoides (MY-ko-PLAZ-ma
My-KOY-dees). This bacterium normally has 901 genes. That’s really not very many.
Quite a few other bacteria, such as E. coli, may have 4,000 to 5,000 genes. People have
more than 22,000 genes, although we don’t need all of them to live and be healthy.
Craig Venter is shown with a DNA-sequencing machines. Using
such devices, he determined the entire genome of the
bacterium M. mycoides, which was then copied in the new
study.
Volker Steger / Science Source
In 2010, researchers at the J. Craig Venter Institute in La Jolla, Calif., copied the entire
genome of M. mycoides. Then they popped it into a cell of a different
species, Mycoplasma capricolum. Some people called this the first synthetic, or
artificial, organism.
More recently, the researchers started by stripping the M. mycoides genome down to its
essentials. Then they transplanted them into the M. capricolum shell. The result was a
minimal bacterium that they now call syn3.0.
The researchers described their results March 25 in Science.
Learning from minimal life
Researchers hope syn3.0’s simple genome will teach them more about the basics of
biology. Minimal life-forms such as this one could also be a starting point for building
custom microbes in the future. These microbes might make certain drugs or chemicals
that people need or prize.
J. Craig Venter is the geneticist who founded the nonprofit institute bearing his name.
He worked with a team of researchers there led by Clyde Hutchison III and Daniel
Gibson. At first, they wanted to design an organism with a core set of about 300 genes.
The researchers thought these would be enough for a microbe to survive on its own.
Computers predicted thus would work. But when the researchers tried to bring their
computer creations to life, “every one of our designs failed,” Venter said in a phone
conference with reporters.
Why didn’t the microbes live? The researchers had left out some genes because they
didn’t know those genes were important.
In fact, scientists don’t know what many genes do. Here, the scientists thought they
already knew the essential ones for survival. They were wrong. Almost one-third of the
genes in the minimal genome are secret ingredients that do something important, even
though scientists don’t know what that something is. Without these genes, the bacteria
died. When the researchers mixed those genes back into their recipe, the bacteria
sprung to life.
An artists’ depiction of DNA. The different colors correspond to
the building blocks that make up long segments that
correspond to genes. Together, they provide the blueprint for
the actions of cells — and, ultimately, an entire organism.
Equinox Graphics / Science Source
Most of those 473 genes in the final recipe do one of four essential jobs. Reading DNA
instructions and turning them into RNA and proteins, is the job of 195 genes. Another
34 genes copy and repair DNA. There are 84 genes involved in building the cell
membrane — the skin around the bacterium — and keeping it working. And 81 genes
carry out metabolism, helping the organism use its fuel for growth and reproduction.
That leaves 149 genes in syn3.0 that do jobs researchers don’t completely understand.
Scientists can predict what 70 of these genes likely do. But what the remaining 79
mystery ingredients do is entirely unknown.
“I think we’re showing how complex life is in even the simplest of organisms,” Venter
says. The results show that researchers still don’t fully understand the basics of life.
“These findings are very humbling,” Venter concludes.
Pamela Silver works at Harvard Medical School in Boston, Mass. As a synthetic
biologist, she designs and creates new types of organisms from genes. Silver says that
lack of knowledge is “frustrating after so many years of molecular biology.” But, she
adds, the new stripped-down microbe may help science learn what those mystery
genes do.
Other researchers have tried to make minimal genomes by stripping away one gene at a
time. Not Venter’s group. His team built its new microbe from the ground up. They made
pieces of DNA from scratch, then combined them into a new genome.
Drew Endy is a synthetic biologist at Stanford University. He is one of several scientists
who like the made-from-scratch approach. “Only when you try to build something do
you find out what’s truly required. Too often in biology we end up with only data, a
computer model, or a just-so story. When you actually try to build something, you can’t
hide from your ignorance,” Endy said in an e-mail. “What you build either works or it
doesn’t.”
And, at first, this bare-bones genome didn’t work. The problem was that the researchers
had compiled a list of genes that they thought they could just leave out. Such genes are
known as nonessential. But not all of those genes proved nonessential after all. Some
genes did the same job as another gene. Researchers could remove one such gene, but
never both at the same time. It’s like a twin-engine jet, Gibson says. Knocking out one
engine will keep the plane airborne, but disabling both engines will lead to a crash.
How low can you go?
The genome of syn3.0 is far smaller than those of any natural free-living bacterium. But
it’s possible that there are life-forms with even smaller starting genomes. For example,
other researchers think it’s possible that there could be some cell hosting just a single
gene inside a membrane. It sole job would likely be to copy RNA, says George Church.
He’s a geneticist at Harvard University.
A newly created microbe called syn3.0. It has the smallest
genome needed to live on its own. Still, scientists don’t know
what almost a third of its essential genes do.
HUTCHISON ET AL/SCIENCE 2016
Researchers might also start with another organism instead of M. mycoides. Or they
might grow bacteria under different conditions. This would probably lead to a microbe
needing a different minimal set of genes, says Jay Keasling. He’s a synthetic biologist at
the University of California, Berkeley. “The minimal genome is in the eye of the
beholder,” he says. It also may depend on the environment, stress or other conditions in
which a life-form will need to survive.
Gibson and Venter agree that they have created a minimal genome, but not
necessarily the most minimal genome. Syn3.0 is streamlined, but still has a few frills.
The team kept several “quasi-essential” genes that may not be strictly necessary. Still,
these genes let the bacteria grow fast enough to be useful in the lab. It is possible that
future minimal life-forms might host even tinier genomes.
Power Words
(for more about Power Words, click here)
bacterium
(plural bacteria) A single-celled organism. These dwell nearly everywhere
on Earth, from the bottom of the sea to inside animals.
cell membrane
Separates the inside of a cell from the outside of it. Some particles
are permitted to pass through the membrane.
computer model A program that runs on a computer that creates a model, or
simulation, of a real-world feature, phenomenon or event.
DNA (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped
molecule inside most living cells that carries genetic instructions. It is built on a
backbone of phosphorus, oxygen, and carbon atoms.In all living things, from plants and
animals to microbes, these instructions tell cells which molecules to make.
E. coli
(short for Escherichia coli) A bacterium that researchers often use to study
genetics. Some types of this microbe cause disease, but many other forms of it do not.
gene (adj. genetic) A segment of DNA that codes, or holds instructions, for producing
a protein. Offspring inherit genes from their parents. Genes influence how an organism
looks and behaves.
genetic
Having to do with chromosomes, DNA and the genes contained within DNA.
The field of science dealing with these biological instructions is known as genetics.
People who work in this field are geneticists.
genome The complete set of genes or genetic material in a cell or an organism. The
study of this genetic inheritance housed within cells is known as genomics.
metabolism The set of life-sustaining chemical reactions that take place inside cells
and bigger structures, such as organs. These reactions enable organisms to grow,
reproduce, move and otherwise respond to their environments.
microbe
Short for microorganism. A living thing that is too small to see with the
unaided eye, including bacteria, some fungi and many other organisms such as
amoebas. Most consist of a single cell.
proteins Compounds made from one or more long chains of amino acids. Proteins
are an essential part of all living organisms. They form the basis of living cells, muscle
and tissues; they also do the work inside of cells. The hemoglobin in blood and the
antibodies that attempt to fight infections are among the better-known, stand-alone
proteins.Medicines frequently work by latching onto proteins.
quasi
A prefix meaning almost, or sort of.
RNA A molecule that helps “read” the genetic information contained in DNA. A cell’s
molecular machinery reads DNA to create RNA, and then reads RNA to create proteins.
symbiosis (adj. symbiotic) A relationship between two species that live in close
contact. A species that lives this way, offering substantial help to the other species, is
sometimes called a symbiont.
synthetic An adjective that describes something that did not arise naturally, but was
instead created by people. Many have been developed to stand in for natural materials,
such as synthetic rubber, synthetic diamond or a synthetic hormone. Some may even
have a chemical makeup and structure identical to the original.
synthetic biology A research field in which scientists work on developing custom life
forms in the lab. Because they make synthetic organisms, scientists who work in this
field are known as synthetic biologists.
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