When setting off on this project, I knew nothing about the new field of evodevo
and all the revolutionary findings that were turning all of biology on its
head. It’s all astoundingly complicated but beautifully logical…Jacques Monod’s
“necessity” in action. And, as much as the endless theme of multilayered
complexity, embryonic development from unfertilized egg to the realization of a
fully functional adult organism exemplifies the phenomenon that I’ve termed
“Natural Design.” Nature finds a way to make living things work—the simplest
and most efficient way…maybe not perfect, but the best way, given all the
physical constraints involved. This section is full of strange terms and
concepts which are intended only to lend a sense of the steps involved in
building a living thing…each one a part of the great web, each a point in time
and the continung evolution of life. So don’t get bogged down in the details.
Just marvel.
X. The Homeobox
Through a variety of experiments,
developmental biologists are beginning to learn how the one-dimensional
information encoded in the nucleotide sequence of a zygote’s DNA is translated
into the three-dimensional form of an animal. There are enough unanswered
questions, however, to entertain many future generations of scientists.
Neil Campbell, Biology (4th ed., 1996)[1]
Neil Campbell, Biology (4th ed., 1996)[1]
As the 21st
century approached, biologists—despite all their remarkable findings—still knew
very little about the specific role of genes in embryonic development. During
the 1970s and 80s, teams of researchers working on different problems were
beginning to understand that regulatory enzymes and genes were responsible for
various aspects of the initial growth phases, including their coordination and
timing.
This
culminated in 1983 with the concurrent discovery (by three separate labs on two
continents) of a cluster, or complex, of regulatory genes responsible for the
orchestration of early developmental stages—the ontogeny—of organisms exhibiting segmented body parts.[2]
Inducing
mutations in these types of creatures by manipulating DNA has, since Morgan’s
time, been an invaluable research
tool—the key to identifying things such as genes’ specific locations on
chromosomes and various of their attributes (for instance, their roles in gene
networks, or whether they were dominant or recessive). The discoveries of the
1980s revealed that various deformities seen in fruit flies—such as extra sets
of wings or legs gruesomely sprouting from heads—were the result of mutations
to groups of genes controlling the fly’s overall body plan. After years of
study, it was found that there were eight of these (what are now known as) homeotic genes in two clusters on one of Drosophila’s
chromosomes. Significantly, the relative position of the genes in these
complexes were found to correspond to the relative head-to-tail order of those
body parts affected. Consequently, it was anticipated that these clusters held
clues to the general logic behind the fly’s body patterning.
When DNA from
the two gene clusters was isolated and analyzed, it was found that proteins
coded for by each of the eight homeotic genes had short sections amounting to
180 nucleotides sharing virtually identical sequences. Researchers
dubbed them homeobox genes.[3]
The abbreviated form, Hox, is still
used in reference to regulatory genes involved with segmentation and related
structures but the term “homeobox” now covers a wide range of genes central to
an organism’s development and growth.
Homeobox genes
are part of what is commonly referred to as the genetic tool kit, which metaphorically consists of a number of
“tools.” Many of these are transcription factors (as mentioned earlier, DNA binding proteins that switch genes on
or off), plus signaling proteins, hormones, and various cellular receptors.
Others include cell-type proteins
(those that determine a cell’s identity) and coloration proteins. Homeobox genes control ontogeny by sending
signals between each other in the form of chemical messengers—gene products—whose transcription they
induce.
Hox genes, again, are identity genes—those responsible for an embryo’s head-to-tail
development. Some delineate the right and left sides of the body; others
establish top and bottom while still others map out general body regions. Hox genes are responsible for switching
on circuit cascades of master genes
such as the homeotic genes that are in charge of building structures associated
with an embryo’s different segments. Homeobox genes, of course, play multiple
roles and virtually never work in isolation.
Here’s an
outline of how this process plays out in the case of that superstar of lab
animals, Drosophila melanogaster:
Like all
arthropods, fruit flies are modular in construction, their bodies arranged in
three sections—head, thorax, and abdomen—which are further subdivided. (For
example: the first thoracic segment bears a pair of legs; the second, another
set of legs plus a pair of wings; and a third carrying the last two legs and a
pair of modified wings—balancing organs called halteres.) Starting with an undifferentiated egg, segments appear
and these become ever more anatomically distinct as development proceeds in a series
of steps determined by gene activation. Regional identity information is
established by the types and, importantly, concentrations
of regulatory proteins that control gene expression. This begins before
eggs are even fertilized.
Egg-polarity genes active in nursery cells surrounding and
nourishing unfertilized eggs in a female fruit fly’s ovary begin the process of defining an embryo’s body axes. When
transcribed, these genes’ mRNA enters the egg cell, remaining near the point of
origin. After being fertilized and laid, the mRNA is translated and its DNA-binding
protein product begins to slowly diffuse though the egg away from its point of
origin, forming a concentration gradient. In the instance of the polarity gene
responsible for establishing anterior-posterior regions in the fertilized egg,
its highest concentration—near the point where it was introduced—delineates the
head end while areas of decreasing concentration sequentially activate segmentation genes that map out
the basic segmentation plan along the anterior-posterior
axis. The dorsal-ventral axis is formed in similar fashion.
After the
major body axes are laid out, three suites
of segmentation genes go to work.
Gap genes determine, in succession, the basic
subdivisions. Next, pair-rule genes establish
pairs of body segments. Finally, segment-polarity
genes set up the front-to-back axis of both halves of the paired segments.
At this point, the boundaries and
orientation of each of the embryo’s segments are permanently
established. The segmentation genes’ protein products, for the most part, are
transcription factors that advance the step-wise system of body plan formation;
in turn, they activate sets of genes that activate other sets, ending with the
homeotic genes that determine the specific anatomy of the embryo’s individual
segments.
The sum total
of an organism’s development is in the delicately balanced timing and sequence
of these master genes being switched on and off, and the duration of their
activation. Molecular biologist Sean Carroll, one of the early leaders in the
field of evodevo, provides glimpses of the remarkably sophisticated logic
employed—yet another exemplary instance of Natural Design on display:
A gene not only may have multiple switches
for different subpatterns of expression at a given time, but will frequently
have different switches that control entirely different states in development.
Tool kit genes are rarely, if ever, devoted to a single developmental
operation. Rather, these tools are used and reused again and again in
development in different contexts to shape the growing embryo. Switches endow
individual tool kit genes with great versatility. Virtually every tool kit gene
is controlled by multiple switches. Ten switches or more is not uncommon, and
we don’t know what the upper limit, if any, may be…. The developmental steps
executed by individual switches and proteins are connected to those of other
genes and proteins. Larger sets of interconnected switches and proteins form
local “circuits” that are part of still
larger “networks” that govern the development of complex structures. Animal
architecture is a product of genetic regulatory network architecture.[4]
Researchers involved with the Drosophila studies that resulted in the initial isolation and
elucidation of Hox genes were
thrilled by their discoveries. Curious to see if other organisms might possess
something analogous, they were shocked to find Hox genes in other animals—barnacles, worms, fish, frogs, mice…and
humans. They found that these genes were positioned on chromosomes in the same
order as in the fly. Researchers were astonished to realize that these
remarkable genes performed the same jobs in each case: specifying the developmental fate of each embryonic
segment in the same head-to-tail order. And it was ascertained that in each
organism, parts of the Hox gene
sequences were virtually identical.
In one famous experiment performed in the 1990s by
Swiss developmental biologist Walter Gehring and his colleagues in Basel, the Hox gene responsible for overseeing the
construction of a fruit fly’s eyes was manipulated so as to be expressed in
different parts of the fly’s body. In this way, eyes were induced to grow on
different flies’ legs, wings, and antennae. Gehring’s team then repeated the
experiment on Drosophila but used a
mouse’s eye-forming gene instead; remarkably, these flies were able to grow normal
eyes. In a similar experiment, the eye-forming gene in a frog was replaced by
the analogous gene in Drosophila and
the frog was also able to grow completely normal eyes. This means that a single
gene product is able to function as a switch that turns on eye development in a
diverse array of animals.
As a result
of these amazing experiments, it now appears that all types of eyes arose from
a common ancestor and that the genes involved are highly conserved and have
been virtually the same for hundreds of millions of years. Until this
discovery, it had been assumed that vision had arisen independently, scores of
times, in creatures as varied as
echinoderms, mollusks, and vertebrates. Apparently, though, the genetic tool
kit was fully emplaced in ancient organisms—distant relatives of all animals
alive today—and that the extremely rapid radiation of forms during the Cambrian
period was merely awaiting favorable ecological conditions that would “light
the fuse.”
©2016 Tim Forsell
10 Apr 2016
[1] Campbell. p 990. (A zygote is a just-fertilized
egg cell.)
[2] The breakthrough —another classic case of the
phenomenon of multiple discovery (see
Shubin, pp 182-83)—was made
independently by researchers at the University of Basel, Switzerland; at
Stanford in California, and Indiana University.
[3] Confusingly, the root “homeo” refers to the sequences’
similarity—not because they’re part of homeotic genes. And “box” is microbiologist
slang for a sequence of identical (or nearly identical) nucleotide bases found
within multiple genes.
[4] Carroll (2005) . pp 123, 129.
