[Paleopsych] NYT: Startling Scientists, Plant Fixes Its Flawed Gene

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Startling Scientists, Plant Fixes Its Flawed Gene
http://www.nytimes.com/2005/03/23/science/23gene.html
March 23, 2005

    By [1]NICHOLAS WADE

    In a startling discovery, geneticists at Purdue University say they
    have found plants that possess a corrected version of a defective gene
    inherited from both their parents, as if some handy backup copy with
    the right version had been made in the grandparents' generation or
    earlier.

    The finding implies that some organisms may contain a cryptic backup
    copy of their genome that bypasses the usual mechanisms of heredity.
    If confirmed, it would represent an unprecedented exception to the
    laws of inheritance discovered by Gregor Mendel in the 19th century.
    Equally surprising, the cryptic genome appears not to be made of DNA,
    the standard hereditary material.

    The discovery also raises interesting biological questions - including
    whether it gets in the way of evolution, which depends on mutations
    changing an organism rather than being put right by a backup system.

    "It looks like a marvelous discovery," said Dr. Elliott Meyerowitz, a
    plant geneticist at the California Institute of Technology. Dr. David
    Haig, an evolutionary biologist at Harvard, described the finding as
    "a really strange and unexpected result," which would be important if
    the observation holds up and applies widely in nature.

    The result, reported online yesterday in the journal Nature by Dr.
    Robert E. Pruitt, Dr. Susan J. Lolle and colleagues at Purdue, has
    been found in a single species, the mustardlike plant called
    arabidopsis that is the standard laboratory organism of plant
    geneticists. But there are hints that the same mechanism may occur in
    people, according to a commentary by Dr. Detlef Weigel of the
    Max-Planck Institute for Developmental Biology in Tübingen, Germany.
    Dr. Weigel describes the Purdue work as "a spectacular discovery."

    The finding grew out of a research project started three years ago in
    which Dr. Pruitt and Dr. Lolle were trying to understand the genes
    that control the plant's outer skin, or cuticle. As part of the
    project, they were studying plants with a mutated gene that made the
    plant's petals and other floral organs clump together. Because each of
    the plant's two copies of the gene were in mutated form, they had
    virtually no chance of having normal offspring.

    But up to 10 percent of the plants' offspring kept reverting to
    normal. Various rare events can make this happen, but none involve
    altering the actual sequence of DNA units in the gene. Yet when the
    researchers analyzed the mutated gene, known as hothead, they found it
    had changed, with the mutated DNA units being changed back to normal
    form.

    "That was the moment when it was a complete shock," Dr. Pruitt said.

    A mutated gene can be put right by various mechanisms that are already
    known, but all require a correct copy of the gene to be available to
    serve as the template. The Purdue team scanned the DNA of the entire
    arabidopsis genome for a second, cryptic copy of the hothead gene but
    could find none.

    Dr. Pruitt and his colleagues argue that a correct template must
    exist, but because it is not in the form of DNA, it probably exists as
    RNA, DNA's close chemical cousin. RNA performs many important roles in
    the cell, and is the hereditary material of some viruses. But it is
    less stable than DNA, and so has been regarded as unsuitable for
    preserving the genetic information of higher organisms.

    Dr. Pruitt said he favored the idea that there is an RNA backup copy
    for the entire genome, not just the hothead gene, and that it might be
    set in motion when the plant was under stress, as is the case with
    those having mutated hothead genes.

    He and other experts said it was possible that an entire RNA backup
    copy of the genome could exist without being detected, especially
    since there has been no reason until now to look for it.

    Scientific journals often take months or years to get comfortable with
    articles presenting novel ideas. But Nature accepted the paper within
    six weeks of receiving it. Dr. Christopher Surridge, a biology editor
    at Nature, said the finding had been discussed at scientific
    conferences for quite a while, with people saying it was impossible
    and proposing alternative explanations. But the authors had checked
    all these out and disposed of them, Dr. Surridge said.

    As for their proposal of a backup RNA genome, "that is very much a
    hypothesis, and basically the least mad hypothesis for how this might
    be working," Dr. Surridge said.

    Dr. Haig, the evolutionary biologist, said that the finding was
    fascinating but that it was too early to try to interpret it. He noted
    that if there was a cryptic template, it ought to be more resistant to
    mutation than the DNA it helps correct. Yet it is hard to make this
    case for RNA, which accumulates many more errors than DNA when it is
    copied by the cell.

    He said that the mechanism, if confirmed, would be an unprecedented
    exception to Mendel's laws of inheritance, since the DNA sequence
    itself is changed. Imprinting, an odd feature of inheritance of which
    Dr. Haig is a leading student, involves inherited changes to the way
    certain genes are activated, not to the genes themselves.

    The finding poses a puzzle for evolutionary theory because it corrects
    mutations, which evolution depends on as generators of novelty. Dr.
    Meyerowitz said he did not see this posing any problem for evolution
    because it seems to happen only rarely. "What keeps Darwinian
    evolution intact is that this only happens when there is something
    wrong," Dr. Surridge said.

    The finding could undercut a leading theory of why sex is necessary.
    Some biologists say sex is needed to discard the mutations, almost all
    of them bad, that steadily accumulate on the genome. People inherit
    half of their genes from each parent, which allows the half left on
    the cutting room floor to carry away many bad mutations. Dr. Pruitt
    said the backup genome could be particularly useful for
    self-fertilizing plants, as arabidopsis is, since it could help avoid
    the adverse effects of inbreeding. It might also operate in the
    curious organisms known as bdelloid rotifers that are renowned for not
    having had sex for millions of years, an abstinence that would be
    expected to seriously threaten their Darwinian fitness.

    Dr. Pruitt said it was not yet known if other organisms besides
    arabidopsis could possess the backup system. Colleagues had been quite
    receptive to the idea because "biologists have gotten used to the
    unexpected," he said, referring to a spate of novel mechanisms that
    have recently come to light, several involving RNA.