杏吧原创

IT IS a voracious predator that devours anything it can fit in its mouth. In
the two weeks of its adult life, it produces up to 350 offspring. It moves with
a surprisingly graceful sinuosity. It even socialises, after a fashion. Yet its
entire body has only 959 cells, while the cells in a human body are numbered in
their trillions. You have probably never seen it, although it or its close
relatives may well browse on the soil-dwelling bacteria in your garden.

This extraordinary creature is the nematode worm Caenorhabditis
elegans, and it is about to make history as the first multicellular
organism whose entire genetic sequence is known. By the end of this year, when
they aim to finish reading all 100 million of the As, Ts, Gs and Cs that spell
out its genetic code, scientists will finally have within their grasp the
complete recipe needed to make an animal. A very small animal, yes鈥擟.
elegans is only a millimetre long鈥攂ut far from insignificant in the
quest to find out not only where genes are but what they do. To understand many
of the mechanisms fundamental to complex life鈥攈ow cells send and receive
signals, how they know where to go and what sort of cell to become during
development, how, when and why they die, why they age鈥攚e probably need
look no further than this tiny creature known to insiders as The Worm.

In the 1960s, Sydney Brenner at the Medical Research Council鈥檚 Laboratory of
Molecular Biology (LMB) in Cambridge was the first to choose C. elegans
as a model animal to study the genetic control of development and the nervous
system. 鈥淪ydney had an eye to select a really superb little experimental system,
and it took off in a much larger way than he expected,鈥� says John Sulston, a
former colleague of Brenner鈥檚 who now jointly heads the worm genome project. The
worm seems tailor-made for lab research. Most of the worms are hermaphrodites,
making it easier to maintain mutant strains. C. elegans grows readily
in laboratory Petri dishes, reaches maturity in only three days, and produces
lots of offspring. Mutants are easy to create and identify for genetic
analysis.

By the late 1980s, Sulston and his colleagues had documented the full
developmental history of every one of the worm鈥檚 959 adult cells, and others had
mapped the approximate location of many of its genes. They began sequencing its
entire genome in 1990. Today Sulston heads the Sanger Centre at Hinxton near
Cambridge, which with the Genome Sequencing Center at Washington University in
St Louis leads the world in human genome sequencing. 鈥淚 think the success of the
worm has been critical in pushing the Human Genome Project along,鈥� says Bob
Waterston, director of the St Louis lab, which has been an equal partner on the
worm sequence since the project began. 鈥淔ive years ago people were saying the
technology is not powerful enough. When we began to sequence a million bases [of
the worm genome] a month, they had to sit up and take notice.鈥�

So what will the complete C. eleganssequence tell us? 鈥淭he genome is
a plan for the full biology of the organism,鈥� says Robert Horvitz, who worked on
the cell lineage with Sulston at the LMB and now runs a large worm lab at the
Massachusetts Institute of Technology in Boston. 鈥淔or example, you don鈥檛 want to
study one member of a family of genes鈥攜ou want to study all of them. Even
with 80 per cent of the genes, you could be missing something.鈥�

The worm has at least 18 000 genes. 杏吧原创s have no idea what half of them
do, but the other half belong to known gene families or closely match genes
discovered in other organisms. Well over 50 per cent of known human genes have a
match in the worm, although that fraction may be artificially high because
researchers sequencing human genes tend to choose genes already known from other
organisms. But the big message reinforced by the worm sequencing project is that
many fundamental biological processes are conserved right the way through
evolution. 鈥淭hat鈥檚 been the revolution of the past ten years of biology,鈥� says
Julie Ahringer, who works on early development in C. elegans at
Cambridge University. 鈥淲e now know that all animals are put together in very
similar ways鈥攈umans, flies, worms and everything.鈥�

What is going to take some explaining is the sheer number of genes that
C. elegans possesses鈥攎any more than are known from the fruit fly
Drosophila melanogaster, for example, even though an entire worm has fewer
cells than a fly has in its eye. 鈥淭hat it鈥檚 got so many genes comes as a
surprise, but in a way it鈥檚 an agreeable surprise because there鈥檚 a lot to
understand there,鈥� says Jonathan Hodgkin of the LMB. For example, the largest
gene families in the worm all make regulatory proteins. These are proteins that
alter the activity of another protein, either directly or by binding to the DNA
and altering how much protein is made. The question is, what are they
regulating?

That鈥檚 the problem that now faces Ahringer in her work on the early worm
embryo. She and her lab are working with a gene called vab-7 that must
be active at a critical point in development to ensure that the skin and muscle
cells in the back half of the worm arrange themselves in neat rows. The protein
made by vab-7 is a transcription factor, a regulatory protein that acts
at the level of DNA. She is now searching for other genes that interact with
vab-7 to map the whole pathway.

In her search she is making use of a new tool called RNA-mediated inhibition,
or RNAi, which has added a further dimension to the worm鈥檚 almost unbelievable
convenience as a laboratory animal. It involves injecting the gonads of
individual hermaphrodite worms with double-stranded RNA corresponding to the
sequence of the gene you want to suppress. Exactly what the RNA does is a
mystery, but worms treated in this way, and their offspring, look for all the
world like mutants in which the gene has been turned off. Once the whole genome
is available, it will be possible to suppress any of the worm鈥檚 genes in this
way, either alone or with others.

Job sharing

By screening worms with a mild vab-7 mutation, Ahringer found an
unrelated gene that enhances vab-7鈥檚 effect. Turning to the genome
database, she searched for genes with a similar sequence to this new gene. She
found one more, making a new gene family with just two members in the worm.
(Each also has a human counterpart.) Using RNAi, she quickly learnt that if she
inactivated one gene, muscle and skin cells were disorganised, while
inactivating the other merely shortened the tail slightly. But inactivating both
left all the embryo鈥檚 tissues disorganised. Standard genetic techniques, which
involve making mutations at random and selecting the ones that seem interesting,
could never have uncovered this kind of shared function among genes. 鈥淩NAi has
really transformed the field. Almost everyone is using it,鈥� Ahringer says.

Another new tool has been developed by people working with the yeast genome
(sequencing completed in 1996) and is now being adapted for the complete worm
genome by Stuart Kim at Stanford University in California. It comprises a DNA
microarray or 鈥渃hip鈥濃�攁 grid of dots of DNA, each representing a gene. All
6000 yeast genes fit on one chip 2 centimetres square, though the worm genome
might need a larger array. Researchers then use a fluorescent dye to label
mRNA鈥攁 messenger molecule produced by active genes鈥攆rom a worm that
has been grown in particular conditions, or is at a certain stage of
development, or has a mutation. Placed in contact with DNA chips representing
the whole genome, the fluorescent RNA molecules selectively bind to their
corresponding DNAs, providing a snapshot of the genes that are active at that
moment. Just by looking at the different patterns of spots, you can see at a
glance how turning off a particular enzyme, for example, affects the expression
of all the other genes.

With techniques such as these, and given the similarity between many worm
genes and genes from other species, biologists are suddenly seeing C.
elegans as a short cut to understanding other organisms. The worm genome is
especially useful because worm researchers have brought about a revolution in
the way sequence data are made available to the scientific community. They broke
with the tradition that no data should be released before publication in a
scientific journal, and instead place each day鈥檚 raw sequence, virtually
straight from the machine, onto a website with free access to all. Today this is
standard practice for publicly funded sequencing projects, hugely accelerating
the rate at which others can use the data. 鈥淭he accessibility has been an
enormous advantage,鈥� says Waterston. 鈥淚t鈥檚 drawing an incredible number of
people into worm biology.鈥�

With the whole sequence on a database accessible via the Internet, finding a
worm relative of a human gene, for instance, now takes just a few minutes at the
keyboard. 鈥淚 get lots of e-mails, phone calls and faxes from people saying the
best match to the gene they鈥檝e cloned is in C. elegans,鈥� says Horvitz.
And it鈥檚 easy to find out what that gene does in the worm. Researchers can make
double-stranded RNA from the worm counterpart of a human gene to see the effect
of suppressing its activity. They can even insert the human gene in place of the
worm gene and see if it functions normally鈥攐r, if the human gene is known
to cause a disease, find out what exactly goes wrong in the worm cells. 鈥淲orms
are wonderful little test tubes for people who work in higher organisms,鈥� says
Cynthia Kenyon, who studies the biology of ageing at the University of
California at San Francisco.

Long live worms

Kenyon and her colleagues have isolated 23 different mutant worms that live
more than twice as long as the normal two or three weeks and have identified
several of the underlying genes. Recently she found that one gene,
daf-2, can control the rate of ageing throughout the whole animal even if
it is turned on in only a few cells. And daf-2 has a counterpart in
humans that makes a receptor for insulin and insulin-like growth factor (IGF-1).
What this means in terms of human ageing is unclear. But, says Kenyon,
laboratory rats that are chronically underfed live longer than rats allowed to
eat all they want鈥攁nd their insulin levels are lower鈥攚hich suggests
that the receptor may also help to determine lifespan in mammals.

The worm has yielded similar parallels between genes that control programmed
cell death, or apoptosis. This is a hot topic: cells may become cancerous
because they fail to die when they should, and degenerative diseases could some
day be treated by turning off cell death genes. Sulston and Horvitz have found
that certain cells in the worm embryo always die during normal development.
Horvitz later identified mutants in which these cells survive in the adult, and
he has pinpointed a number of genes that control the death mechanism. At least
five have counterparts that control cell death in humans.

杏吧原创s armed with the worm鈥檚 complete genome may even be able to learn
some of the secrets of human behaviour. Last May, Hodgkin reported that strains
of C. elegans collected in the wild showed two distinct behaviours when
placed in a laboratory dish full of Escherichia coli bacteria, their
standard laboratory diet. Some strains moved quickly until they encountered
other worms, then 鈥渃lumped鈥� into writhing heaps. Others moved more slowly and
studiously ignored each other, spreading out over the whole surface. In
September, Mario de Bono and Cornelia Bargmann at the University of California
at San Francisco traced the origin of the two behaviours to a single amino acid
difference in one receptor protein. And yes, the protein does have a human
counterpart: a receptor for a neurotransmitter, neuropeptide Y, that is involved
in eating, mood, memory and blood pressure.

It is too soon to jump to conclusions about the control of human social
behaviour, but Hodgkin finds the result intriguing. 鈥淲hat this work does is to
give you an entry point into understanding what one might think of as a fairly
sophisticated piece of behaviour. And maybe because we understand so much about
the nervous system of C. elegans and have all these tools available,
one can work out in detail everything that鈥檚 going on there.鈥�

But Hodgkin cautions that even the most sophisticated laboratory analyses may
never lay bare all the worm鈥檚 secrets. 鈥淲e grow C. elegans in the lab,
and we feed it E. coli, which is a bacterium that it never ever
encounters in the wild, so it鈥檚 living in a totally unnatural environment,鈥� he
says. 鈥淎nd yet we have the impertinence to suggest that we鈥檙e maybe going to
understand everything about it by having its 100 million base pairs. It ain鈥檛
so! There are so many things going on out there in the wild that undoubtedly we
are never going to see in the lab, but which are crucially important to how the
whole organism lives and interacts with its environment.鈥�

The ranks of scientists working in nematode research have swelled from their
small, friendly beginnings when the sequence began to roll out of the machines
in St Louis and Cambridge. If you add in all those human biologists who have
started collaborations with worm people, the number reaches tens of thousands.
This vindicates the view Sulston always held, that even if the project was
expensive, it would ultimately be good value for money. He is currently trying
to close the last few intractable gaps in the worm genome sequence. 鈥淚t鈥檚 worth
pursuing to the end,鈥� he says. 鈥淚 have no doubts at all about that. It鈥檚 going
to go on being mined forever and it鈥檚 delivering more value every year.鈥�