Download Chapter 19 Questions

Chapter 19 Answers
1.
See Figure 19-2 for the relative genome contents of these animals. In general, vertebrates
such as pufferfish, mice, and humans have on the order of 30,000 genes, and invertebrates such
as nematodes and insects have around 15,000.
The additional genes seen in vertebrates are usually the result of gene duplication and
divergence, rather than the creation of entirely new genes. This is known because most vertebrate
genes have a counterpart in invertebrate genomes.
2.
The evidence for the key role of Pax6 in eye development comes from dramatic
experiments in which the gene is abnormally expressed in other, non-eye tissues. When Pax6 is
expressed, for example, in Drosophila tissues that would normally give rise to wings or legs,
eyes develop instead.
A single gene such as Pax6 can trigger the development of a structure as complex as the
eye because it can bind to and regulate multiple target genes. The target genes of a master
regulatory molecule such as Pax6 likely include some encoding proteins that are specifically
related to eye function (such as the rhodopsins, which are involved in the detection of light),
others encoding general cellular functions (such as proteins regulating the cell cycle and/or
cellular differentiation), and others encoding patterning molecules that help organize the tissue in
the intricate way that is required for the formation of the eye.
The same regulatory gene can be used to direct the formation of related but distinct
structures in different organisms for several reasons. First, differences in the expression pattern
of the regulatory genes themselves can produce differences in the overall morphology of the
structures (for example, differences in the pattern of Pax6 expression appear to underlie some
differences in eye morphology between different organisms). Also, the regulator's target genes
will differ between organisms, both in terms of their expression patterns (for example, because of
alterations in their cis-regulatory regions) as well as in their activity (for example, because of
differences in their amino acid sequences). Finally, the development of a structure does not take
place in a vacuum, and can be influenced by other, overriding differences between the tissues
that are used to make the structures. For example, the cells that are used to make a fly eye differ
in numerous ways from those used to make a mouse eye—such as in their gene expression, their
morphology, and their cellular environment.
3.
One possibility is that the squirtless gene is not expressed in the pheromone-producing
segment of the tree flirt, allowing the segment to produce this structure rather than a squirt gland.
A second possibility is that the gene is expressed in the segment, but that the amino acid
sequence of the encoded protein is different in the tree flirt, and so it activates a different set of
target genes. A third possibility is that the squirtless genes encode identical proteins in the two
organisms, but that the cis-regulatory regions of the proteins' target genes have been altered in
the tree flirt, leading to different patterns of target gene expression.
There are several ways in which you could experimentally distinguish between these
possibilities. First, you could examine the expression pattern of the squirtless gene in the tree
flirt, to see if it is expressed in the pheromone-producing segment. If it is not, this would suggest
that the first possibility is correct, something you could confirm by introducing a transgene into
the tree flirt that causes the squirtless gene to be expressed in that segment. If the first possibility
is indeed correct, this should cause a squirt gland to be produced instead of the pheromone
producing structure. In addition, if you discover that the squirtless gene is in fact normally
expressed in the pheromone-producing segment, you could replace the tree flirt squirtless gene
with that from the tree squirt. If this causes a squirt gland to be produced instead of the
pheromone-producing structure, this would be evidence for the second possibility, namely that a
difference in protein activity underlies the difference in segmental identity. In contrast, if you
discover that introducing the tree squirt gene into tree flirts produces no change in segmental
identity, this would suggest that the two Squirtless proteins are functionally identical, and that
the third possibility is the correct one.
4.
Fruit flies have one pair of wings and one pair of halteres, in contrast to dragonflies,
which have two pairs of wings.
If the gene X is identical in terms of its encoded amino acid sequence as well as its
expression pattern, then the difference in gene X function between the two organisms must result
from differences in gene X's target genes. For example, if gene X produces a repressor that is
expressed in the hindwings of fruit flies to inhibit the expression of a wing-specific gene
(causing halteres to develop instead), the cis-regulatory region of the wing-specific gene could be
altered in dragonflies so that the gene X repressor can no longer bind there. This would permit
the wing-specific gene to be expressed in the dragonfly hindwing, thereby allowing wings to
develop.
5.
You could ask whether the vertebrate gene can also specify leg development in insects by
expressing it in insects. For example, you could replace the coding sequence of the insect gene
with the coding sequence of the vertebrate gene. In this way, the vertebrate gene would be
expressed in vivo in the precise pattern in which the insect gene is normally expressed. If the
transgenic insect develops normal legs, then you can conclude that the vertebrate gene can
indeed specify insect leg development.
If the vertebrate gene works in insects, this would suggest that the overall logic of leg
development has been conserved between invertebrates and vertebrates. It would also indicate
that the differences between the vertebrate and insect legs are not the result of a difference in the
activity of the protein that specifies leg development. Instead, the difference is likely to result
from changes in the expression pattern of the leg-specifying gene, and/or from differences in the
regulation or activity of its target genes.
This kind of experiment, in which a pattern determining gene from one organism is
replaced with an analogous gene from another organism, can be useful for distinguishing
between the possible strategies for altering the activity of pattern determining genes. For
example, if you find that a particular patterning gene is expressed in equivalent tissues in two
different organisms, but the tissues develop into different structures, you can exchange the genes
between the organisms to see if this has any effect on which structure is produced in which
organism. If exchanging the genes alters the identity of the structures produced, you can
conclude that the developmental difference is due to differences in the activity of the proteins
encoded by the genes. If, on the other hand, the two genes can be swapped with no effect, you
can conclude that the difference is due to differences in the proteins' target genes, rather than in
the proteins themselves.
6.
The functional differences between ftz and Antp stem from two sources. First, the cis-
regulatory regions of the two genes differ leading Antp to be expressed in a single band located
where the mesothorax will develop, and ftz to be expressed in seven stripes that help subdivide
the embryo into segments. The Ftz and Antp proteins also differ, in that they interact with
distinct partner proteins that cause them to bind to different sites on the DNA. Because of this
difference in their DNA binding specificities, Ftz and Antp regulate distinct sets of target genes.
7.
A single nucleotide change within each of the two Dorsal binding sites is sufficient to
convert the binding sites into optimal recognition sequences, allowing expression of the reporter
gene throughout the presumptive mesoderm.
An additional eight nucleotide substitutions can create two Twist binding sites within the
enhancer, allowing expression in the neurogenic ectoderm; therefore a total of 10 nucleotide
changes can bring about expression throughout the mesoderm and the neurogenic ectoderm.
Finally, altering 12 nucleotides within the enhancer can create binding sites for
Daughterless, which, together with the two nucleotide changes that create optimal Dorsal binding
sites (for a total of 14 nucleotide changes), cause the reporter gene to be expressed in lateral
stripes.
The fact that 2, 10, or 14 nucleotide changes out of 200 can produce such radical
alterations in gene expression indicates that changes in cis-regulatory regions are a very powerful
way of altering patterning gene activity, perhaps even more powerful than are alterations in
coding sequences. This suggests that such changes may play a major role in the evolution of
gene function.
8.
a.
2nd segment: Antp expressed, mesothorax; 3rd segment: Ubx expressed,
metathorax.
b.
2nd, 3rd segments: Antp expressed, mesothorax.
c.
2nd, 3rd segments: Ubx expressed, metathorax.
d.
2nd, 3rd segments: Ubx expressed, metathorax.
e.
2nd, 3rd segments: Antp expressed, mesothorax.
f.
2nd, 3rd segments: Ubx expressed, metathorax
g.
2nd, 3rd segments: Ubx-VP16 expressed, mesothorax.
9.
The presence of the tetrapeptide motif YKWM suggests that the protein interacts with
Exd in order to bind to its target sites on the DNA.
Both Ubx and Antp contain a similar motif.
The binding sites for different Exd-containing heterodimers are similar, differing
primarily in terms of the spacing between the "half-site" recognized by Exd and the half-site
recognized by the other protein. Changing the spacing between the binding sites can alter its
binding affinities: reducing the spacing between the Antp and Exd half-sites within an Antp-Exd
binding site, for example, allows the site to be bound by Ubx-Exd dimers.
10.
The order of the genes within the Bithorax complex is colinear with their pattern of
expression in the embryo. Specifically, the order of genes in the complex is Ubx– abd-A–Abd-B
(with Ubx at the 3' most position) and they are expressed in the same order in the embryo (with
Ubx expressed most anteriorly, then abd-A, then Abd-B in the posterior-most region).
This colinearity of genome position and expression pattern for the homeotic genes is
conserved throughout the animal kingdom.
Although the significance of the colinearity is not well understood, inverting the entire
complex should not change the pattern of expression of the genes, as they are primarily
controlled by cis-regulatory sequences located close to the genes.
11.
"Posterior prevalence" refers to the repression by posterior Hox genes of more anterior
Hox genes.
For example, in Drosophila, Ubx is expressed in the third thoracic segment, and represses
the expression of Antp. Antp is expressed in the second thoracic segment, where Ubx is not
present. In vertebrates, a similar example is provided by Hoxc-6 and Hoxc-8. Hoxc-8 is
expressed in the lumbar vertebra, where it represses Hoxc-6 expression. Hoxc-6 is expressed in
the more anterior thoracic vertebrae, where there is no Hoxc-8.
12.
You predict that Scr is expressed in the first and second thoracic segments, and that Ubx
is expressed in the third through fifth segments.
13.
Ubx represses Dll expression in the abdomen of flies, but has no effect on Dll expression
in the abdominal segments of crustaceans.
In flies, the repression of Dll in the abdominal segments blocks the development of limbs
in the segments. In crustaceans, in contrast, the absence of Dll repression in the abdomen allows
limbs to form.
The difference in Ubx protein function between flies and crustaceans was demonstrated
by expressing either the fly or the crustacean Ubx protein in fly embryos. Whereas Ubx from
flies repressed Dll expression throughout the presumptive thorax (and prevented any limbs from
developing), the crustacean Ubx had no inhibitory effect on Dll expression.
14.
Ubx is expressed in the hindwings of both dipterans and lepidopterans, yet dipterans
produce halteres in that segment and lepidopterans produce a second pair of wings. The basis for
this difference is not in the activity of the Ubx protein in the different organisms, but rather in the
cis-regulatory DNA of the protein's target genes. This was demonstrated by expressing the
butterfly (lepidopteran) Ubx protein in flies, where it was perfectly capable of inhibiting wing
development just as the fly Ubx protein normally does.
It makes sense that changes in cis-regulatory regions might underlie many evolutionary
changes, because they can rapidly produce major changes in gene expression patterns. Changing
just 14 nucleotides within the 200 base pair twist enhancer in Drosophila, for example, can
radically change the expression pattern of a reporter gene linked to the enhancer. In contrast, it is
much less efficient to change the activity of patterning proteins by simply changing their amino
acid sequences. Often, patterning proteins from different organisms share only limited sequence
homology, yet are entirely capable of substituting for one another and carrying out their
respective functions.
15.
The same number of genes can give rise to different levels of complexity because
complexity is determined more by the total number of different gene expression patterns than by
the total number of genes. Therefore, if the average human gene has more distinct enhancers than
the average mouse gene, then humans will have more distinct gene expression patterns than
mice. This could serve as the basis for the greater complexity of humans.
16.
FoxP2 is a DNA-binding protein that has been implicated in human speech. The protein
has also been found in other animals, such as mice and chimpanzees, although the human form
of the protein differs from the other forms at certain key amino acids.
FoxP2 was first identified as a speech related gene because mutations in the gene cause
speech defects in humans.
Although FoxP2 appears to play an important role in human speech, human language
ability is an enormously complex process that is surely based upon more than the handful of
amino acid differences that separate the human and mouse FoxP2 proteins. Accordingly,
expressing the human FoxP2 gene in mice would be unlikely to have any major impact on the
language ability (or lack thereof) of the mice.
Similarly, there are likely to be numerous differences in the coding sequences and
expression patterns of key genes involved in language acquisition between humans and
chimpanzees. Accordingly, it is unlikely that expression of human FoxP2 would enable
chimpanzees to talk (although it may very well have more of an effect on their language ability
than it would on mice).
17.
The human and chimpanzee genomes are remarkably similar, differing by about 2%. It is
likely that, given the similarity between the human and chimpanzee genomes, many of the
important differences between the two genomes will be in cis-regulatory regions of certain
critical genes. Changes within these regions could bring about important differences in certain
gene expression patterns between humans and chimpanzees, serving as the basis for many
morphological and behavioral differences between the two primates.