How Many Genes Do Cells Need? Maybe Almost All of Them
An ambitious study in yeast shows
that the health of cells depends on the highly intertwined effects of many
genes, few of which can be deleted together without consequence.
https://www.quantamagazine.org/how-many-genes-do-cells-need-maybe-almost-all-of-them-20180419/
The activities of genes in
complex organisms, including humans, may be deeply interrelated.
April 19, 2018
By knocking out genes three at a
time, scientists have painstakingly deduced the web of genetic interactions
that keeps a cell alive. Researchers long ago identified essential genes that
yeast cells can’t live without, but new work, which appears today inScience, shows that
looking only at those gives a skewed picture of what makes cells tick: Many
genes that are inessential on their own become crucial as others disappear. The
result implies that the true minimum number of genes that yeast — and perhaps,
by extension, other complex organisms — need to survive and thrive may be
surprisingly large.
About 20 years ago, Charles Boone and Brenda Andrews decided to do something
slightly nuts. The yeast biologists, both professors at the University of
Toronto, set out to systematically destroy or impair the genes in yeast, two by
two, to get a sense of how the genes functionally connected to one another.
Only about 1,000 of the 6,000 genes in the yeast genome, or roughly 17 percent,
are considered essential for life: If a single one of them is missing, the
organism dies. But it seemed that many other genes whose individual absence was
not enough to spell the end might, if destroyed in tandem, sicken or kill the
yeast. Those genes were likely to do the same kind of job in the cell, the
biologists reasoned, or to be involved in the same process; losing both meant
the yeast could no longer compensate.
Ignorant as science may still be
about certain happenings in yeast, it’s dwarfed by our ignorance of what is
going on in our own cells
Boone and Andrews realized they
could use this idea to figure out what various genes were doing. They and their
collaborators went about it deliberately, by first generating more than 20
million strains of yeast that were each missing two genes — almost all of the
unique combinations of knockouts among those 6,000 genes. The researchers then
scored how healthy each of the double mutant strains was and investigated how
the missing genes could be related. The results let the researchers sketch a
map of the shadowy web of interactions that underlie life. Two years ago,
they reported the details of the map and revealed
that it had already allowed researchers to discover previously unknown roles for genes.
Along the way, however, they
realized that a surprising number of genes in the experiment didn’t have any
obvious interactions with others. “Maybe, in some cases, deleting two genes
isn’t enough,” Andrews said, reflecting on their thoughts at the time. Elena
Kuzmin, a graduate student in the lab who is now a postdoc at McGill
University, decided to go one step further by knocking out a third gene.
In the paper out today in Science, Kuzmin,
Boone, Andrews and their collaborators at the University of Toronto, the
University of Minnesota and elsewhere report that effort has yielded a
deeper and more detailed map of the cell’s inner workings. Unlike in the double
mutant experiments, the researchers did not make every possible combination of
mutations — there are about 36 billion different ways to knock out three genes
in yeast. Instead, they looked at the pairs of genes they’d already knocked out
and ranked their interactions according to severity. They took a number of
those pairs, whose effects ranged from making cells grow a little slower to
making them significantly impaired, and matched them up one by one with
knockouts of other genes, generating about 200,000 triple mutant strains. They
monitored how quickly colonies of the mutant yeast grew, and after noting which
mutants were struggling, they checked databases to see what the disabled genes
were thought to do.
Charles
Boone and Brenda Andrews, genomics researchers at the University of Toronto,
oversaw the effort to systematically delete pairs and triplets of genes
from yeast cells for insights into the genes’ functions. They found that even
seemingly unrelated genes can have crucially interconnected effects.
Michael Schertzberg
As the scientists built their new
map, several things became clear. For one, in about two-thirds of the triple
mutants that showed an additional genetic interaction, knocking out the third
gene tended to intensify the problems that the double mutant had. Pairs of
genes might already show some interaction with each other, Andrews said, “but
it was much more severe when we deleted a third gene.” Boone says that these
are likely to be situations in which the loss of a third gene is dealing a
critical blow to an already faltering system.
However, a third of the
interactions were completely new. And they tended to involve more disparate
processes. In double mutants, the functional connections between genes tended
to be tight: A gene involved in DNA repair usually had links with other genes
that are also involved in DNA repair, and genes that had interactions with each
other usually interacted with the same other genes. With the triple mutants,
however, more far-flung tasks started to get linked together. The constellation
of connected cellular tasks shifted and morphed subtly.
“Perhaps what we’re sampling here,”
Andrews said, “are some functional connections in the cell that we weren’t able
to see before.”
One set of new connections, for
example, was between genes involved in transporting proteins and genes involved
in DNA repair. On the surface, it’s difficult to see what would connect these
two functions. And in fact, the researchers still don’t have a mechanistic
explanation. But they are sure there is one. “Our immediate reaction was,
‘Well, that’s kind of random,’” Andrews said. “But we’ve learned over the
course of doing this project that it’s not random. We just don’t understand how
the cell is connected.”
Their group has just started
probing that link between protein transport and DNA repair, but according to
Andrews, if you look closely at those yeast cells, they do in fact show a great
deal of DNA damage. The map of connections helped draw their attention to it:
“There would have been no reason to look before,” she said.
Yeast geneticists were never
under the impression that only essential genes mattered. But the new paper
reinforces the idea that simplistic interpretations of just what is important
in the yeast genome are likely to be flawed. The reality is more complicated,
Boone and Andrews say. They suggest that when double and triple interactions
are taken into account, the number of genes that a yeast cell truly can’t do
without jumps. As their paper notes, the minimum genome needed for yeast cells
to avoid a substantial defect “may nearly approach the complete set of genes
encoded in the genome.”
This
figure maps the interactions among various genes (represented as dots) in the
yeast genome. Genes with linked effects are connected by lines; genes with more
strongly correlated effects are closer together. The color of the dots
corresponds to the biological processes and organelles in which the genes are
involved.
Anastasia Baryshnikova,
University of Toronto
Indeed, experimental efforts to
devise a minimal genome for a microorganism — to pinpoint the smallest number
of genes that a cell would need to survive, as a step toward making artificial
genomes — have shown it to be surprisingly difficult to remove genes and still
have a thriving creature.
In 2016, researchers at the J.
Craig Venter Institute (JCVI) reported the creation of an artificial genome for
the bacterium Mycoplasma genitalium, in which they winnowed
its 525 genes down to 473. But negative effects from removing seemingly
inessential genes were indeed a serious issue, according to Clyde A. Hutchison III, a biochemist and
distinguished professor at JCVI involved in the work. “That was the main
problem for choosing a gene set to design for a minimal genome,” he said.
Joel Bader, a systems biologist at Johns Hopkins
University, says that the current work suggests an intriguing connection to an
idea in human genetics — that a wide array of genes may be subtly
influencing traits that we don’t normally associate with them.
“[The] closer we are able to look, the more we are able to see that perturbing
one gene or pathway has effects that propagate throughout the entire system,”
he said. “The effects get weaker, but they can still be measured.”
Ignorant as science may still be
about certain happenings in yeast, it’s dwarfed by our ignorance of what is
going on in our own cells. Part of what makes a project like this one at the
University of Toronto possible is that yeast has been heavily studied and its
genes intricately annotated by several generations of biologists, to a degree
not yet reached with the human genome, which is comparatively enormous,
rambling and full of mysteries. Still, the researchers say that they hope that
as gene-editing technology for human cells advances, these kinds of experiments
can help reveal more about the workings of cells and how the genes within a
genome relate to one another. “I think there are many basic rules of genome
biology we have not discovered,” Andrews said.
Correction: This article was
updated on April 20 to include mention of the contributions of scientists
at the University of Minnesota to the new Science paper. The credit
for the map of gene interactions was also corrected on April 23 to read
“Anastasia Baryshnikova, University of Toronto.”
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