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Monday, July 10, 2017
Scientists catch plants changing chemistry thought to be immutable
If there was ever a proof of directed change, here it is. Blaming this on any form of chance is silly. Particularly now that we understand the central role of the spirit body in each cell as a processor and control system. It even looks like a computer.Until we fully understand the central role of the cellular processor, we will be running blind. This processor is a three dimensional mass of dark matter holding information through 2 D ribbons forming Mobius strips and containing information. It acts by encoding electrons belonging to the molecules.That means that GOD, whatever you wish to think that means, but should not really be thought as Anthropomorphic in all fairness, can conduct almost any plausible experiment it wishes and does because it is truly forward thinking and not stuck in time as we are.. ..
Scientists catch plants in the act of changing chemistry thought to be immutable because necessary for life
Because plants can't get up and run away, they've had to be clever
instead. They are the chemists of the living world, producing hundreds
of thousands of small molecules that they use as sunscreens, to poison
plant eaters, to scent the air, to color flowers, and for much other
secret vegetative business.
Historically these chemicals, called "secondary metabolites,"
have been distinguished from "primary metabolites," which are the
building blocks of proteins, fats, sugars and DNA. Secondary metabolites
smooth the way in life but the primary metabolites are essential, and
the failure to make them correctly and efficiently is fatal.
Secondary metabolism is thought to have evolved to help plant
ancestors deal with living on dry land rather than the more hospitable
oceans. The idea is that the genes for enzymes in the molecular assembly
lines of primary metabolism were duplicated. The duplicates were more
tolerant of mutations that might have destabilized the primary pathways
because the originals were still on the job. With evolutionary
constraints thus relaxed, synthetic machinery was able to accumulate
enough mutations to do new chemistry.
Primary metabolism, however, is widely conserved, meaning that it
remains unchanged across many different groups of organisms because it
has been fine tuned to operate correctly and efficiently and because its
products are necessary for life. Or so the textbooks say.
But now a collaborative team of scientists has caught primary
metabolism in the act of evolving. In a comprehensive study of a
primary-metabolism assembly line in plants, they discovered a key enzyme
evolving from a canonical form possessed by most plants, through
noncanonical forms in tomatoes, to a switch-hitting form found in
peanuts, and finally committing to the novel form in some strains of
This feat, comparable to pulling the tablecloth out from under the
dishes without any breaking any of them, is described in the June 26
issue of Nature Chemical Biology. It is the work of a
collaboration between the Maeda lab at the University of Wisconsin,
which has a longstanding interest in this biochemical pathway, and the
Jez lab at Washington University in St. Louis, which crystallized the
soybean enzyme to reveal how nature changed how the protein works . "The work captures plants in the process of building a pathway that
links the primary to the secondary metabolism," said Joseph Jez, the
Howard Hughes Medical Institute Professor in the Department of Biology
in Arts & Sciences. "We're finally seeing how evolution creates the
machinery to make new molecules."
It may also have practical importance because the old and the new
pathways make the amino acid tyrosine, which is a precursor for many
secondary metabolites with biological and pharmaceutical activity—
everything from vitamin E to opioids. But the old pathway makes only
tiny amounts of these compounds, in part because they must compete for
carbon atoms with the greedy process for making lignin, the tough
polymers that let plants stand tall.
The discovery of the new pathway for making tyrosine is much less
constrained than the old one. This raises the possibility that carbon
flow could be directed away from lignin, increasing the yields of drugs
or nutrients to levels that would allow them to be produced in
commercial quantities. A tale of two enzymes Tyrosine is made on an assembly line called the shikimate pathway, a
seven-step metabolic pathway that plants use to make the three amino
acids that have aromatic rings. Animals (including people) shed the
ability to erect this assembly line deep in the evolutionary past.
Because we cannot make these amino acids on our own and they are
essential for life, we must instead obtain them by eating plants or
That aromatic ring is important, said Jez, because it is a
distinctive structure that can absorb light or energy. So the aromatic
amino acids also are the precursors for many secondary metabolites that
capture light, transfer electrons, or color flowers. Moreover, the
aromatic amino acids are also precursors for chemicals that poison other
plants or plant predators and attract pollinators. Many medicinal drugs
include an aromatic ring, Jez commented.
In most plants the shikimate pathway is in the chloroplast, the
organelle that does the work of converting the energy of sunlight to
energy stored in carbon bonds. Once made, however, tyrosine can be
exported out of the cytosol for incorporation or conversion into other
In the last step of one branch of the pathway an enzyme called
arogenate dehydrogenase (ADH), catalyzes a reaction that makes the
compound arogenate into tyrosine. The ADH enzyme is considered
"regulatory" because it is a bottleneck in tyrosine production. It must
compete for the arogenate substrate with the branch of the shikimate
pathway that makes a different aromatic amino acid and it is strongly
inhibited by the buildup of tyrosine
ADH activity is common in plants, but in the course of studying the
shikimate pathway the Maeda lab discovered that the DNA sequences coding
for ADH in some flowering plants were significantly different from
those in most plants. They called the enzymes produced by these
sequences noncanonical ADH. Then, in 2014, they reported that some
legumes also make tyrosine with a different enzyme, called prephenate
PDH differs from ADH in many ways. It is active outside the
chloroplast, it acts on the substrate prephenate rather than on
arogenate, because it is outside the chloroplast it does not have to
compete for its substrate with other branches of the shikimate pathway,
and it is not inhibited by rising levels of tyrosine.
Why are there two different assembly lines for tyrosine? The
scientists believe the PDH enzyme evolved via two gene duplication
events and the accumulation of mutations in the "extra" copies of the
gene. The first event gave rise to nonstandard ADHs in some flowering
plants and the second to PDH in a subset of legumes. But why did this
That's not a question the scientists can answer yet except in general
terms, Jez said. What sticks out, however, is that the more recently
evolved metabolic pathway is not tightly regulated and could potentially
churn out product at a hectic pace. Perhaps the legumes were in dire
need of secondary metabolites for some reason. It is certainly
suspicious that legumes have an ecology quite different from that of
other plants, since they live symbiotically with nitrogen-fixing
bacteria. Fiddling the bits
By this point the scientists knew that the novel enzyme, PDH, bound a
different substrate than the original enzyme, ADH. They also knew that
PDH, unlike ADH, did not bind tyrosine itself. But what changes in
structure led to these differences in chemical activity?
To find out, Craig Schenck, a graduate student in the Maeda lab,
compared the gene sequences for the ADH or PDH enzyme in many different
plants, carefully chosen to be on the boundaries of the switchover from
one enzyme to the other. But they encountered a problem. There were
enough differences in the DNA that it was difficult to see what was
relevant, Jez said.
Encountering Maeda at a conference, Jez offered to try crystallizing
the novel enzymes so that their structure could be reconstructed from
X-ray images. His graduate student Cynthia Holland was able to
crystallize the soybean PDH and produce detailed images of its
"Once you looked at the structure you could see that there were only
two differences from the typical ADH found in most plants and only one
of the differences actually changed things," Jez said. Stunningly that
difference was a single amino acid in the active site on the enzyme. At
that spot the asparagine had replaced aspartic acid.
Schenck double-checked this structural insight by flipping that amino
acid in mutant forms of the enzyme. The ADH mutant turned out to have
PDH activity, and the PDH mutant had ADH activity, just as the team had
"That one difference changes the enzyme's preferred substrate and its
ability to be inhibited by tyrosine feedback," Jez said. "And if you
look at it, it's literally the difference between a nitrogen atom or an
oxygen atom. In these proteins, which are made up of nearly three
hundred amino acids or forty-two hundred atoms, one atom makes all the
difference. That's just kind of cool."
The work is important because it demonstrates that primary metabolism
does evolve. And because it shows how nature steals machinery from
primary metabolism and cobbles it together for making novel secondary
metabolites. They do this with much more finesse than genetic engineers
can yet manage.
"When we want a plant to make a new molecule," Jez said, "we drop in a
gene and hope it integrates with existing pathways. We still don't know
how to readily connect the wiring between what we drop in and what is
already there. So it is interesting to see how nature contrived to
connect the wiring and change things without breaking them."
More information: Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants, Nature Chemical Biology (2017). DOI: 10.1038/nchembio.2414Provided by: Washington University in St. Louis