Download Differential Gene Expression in Development

Regulation of Development
Slide 2
The development of multicellular organisms from a zygote to the adult
form is a highly regulated process. Cells respond to developmental signals in order to
differentiate into the mature cell types of the organism, and form the tissues and organs
that make up the adult body. In many instances, the bodies of organisms develop as
integrated segments. Clear examples of this are organisms like earthworms or centipedes
and many plants, which consist of numerous, clearly defined, and fairly similar segments.
Other organisms, such as the fruit fly, contain segments that are not so clearly identified
at first glance. Adult flies, for example, are actually made of thirteen segments, groups of
which are fused to form the head, thoracic, and abdominal portions of the body. Even
humans exhibit segmentation in the form of the vertebrae composing the spinal column.
The formation of segments, hence the development of the mature form of the organism, is
controlled by different sets of genes acting in a sequential manner. As organisms develop,
the differential expression of these genes allows for finer and finer development of each
segment until the entire organism is formed.
As we will see, the pathways of segmentation provide key insights into pattern formation
and the development of organisms, as well as the evolutionary history of organism
development. In this lesson, we will look at genes that regulate development in animals,
using the fruit fly as an example, and plants, using Arabidopsis as an example.
Slide 3
In animals, the formation and refinement of body segments is controlled
by different groups of genes. These groups of genes do not all act at once, but rather in
sequence, with some of the products from a group of genes controlling the transcription
or translation of the genes of the next group. This sequence is referred to as a regulatory
cascade, as each group of genes regulates the activity of the next. In the fruit fly,
Drosophila melanogaster, there are three basic types of genes in the regulatory cascade:
maternal effect genes, segmentation genes, and homeotic genes. Maternal effect genes are
active in maternal cells, or cells of the mother fly, that surround the egg and developing
embryo. The other four groups of genes are expressed after the embryo has developed to
contain around 6000 free nuclei, and are active throughout the rest of embryonic
development.
Slide 4
Maternal effect genes code for cytoplasmic determinants that determine
the polarity of the egg and early developing embryo. Specifically, the protein products of
these genes determine the dorsal-ventral and anterior-posterior axes of the developing
embryo. Two maternal effect genes in particular, the bicoid and nanos genes, play wellunderstood roles in determining the polarity of the embryo. Prior to fertilization, mRNAs
made from both of these genes are translocated from maternal cells to the egg cell.
However, the concentration of these mRNAs differs from one end of the cell to the other.
Bicoid mRNA is concentrated at one end of the egg, while nanos mRNA is concentrated
at the other. The end with the higher concentration of bicoid mRNA will eventually
become the anterior end of the embryo and mature fly, while the end with a higher
concentration of nanos mRNA will become the posterior end of the fly. After fertilization
of the egg, the mRNA for the bicoid and nanos genes are translated into protein, so that a
protein gradient now exists within the embryo: bicoid protein at the anterior end and
nanos at the posterior end. Each of the proteins now acts to control the expression of the
segmentation genes that follow the maternal effect genes in the regulatory cascade. These
proteins do this primarily by affecting the transcription of segmentation genes or the
activity of the proteins coded for by segmentation genes.
Slide 5
Segmentation genes include three classes of genes that further refine the
development of the Drosophila embryo – gap genes, pair rule genes, and segment
polarity genes. Gap genes are the first segmentation genes in the Drosophila regulatory
cascade. As mentioned on the previous slide, the activity of gap genes is largely
controlled by the transcription factor activity of maternal effect genes. Gap genes define
broad areas along the anterior-posterior axis of the developing embryo. Mutations in gap
genes result in embryos that develop with several segments missing (a ‘gap’ in the body).
Some products of gap genes act as transcription factors that affect the transcription of the
next class of genes in fruit fly development, the pair rule genes.
Pair rule genes begin to define the location of segments by dividing the embryo into units
representing two future segments each. Some of the protein products of pair rule genes
also control the expression of segment polarity genes and homeotic genes, which
represent the next steps in the regulatory cascade. Are you beginning to see a pattern
here?
Segment polarity genes sharply define the borders of the segments of the embryo, and
begin to organize the different areas within each segment, as the embryo becomes more
and more refined. Segment polarity proteins also affect the differential expression of
homeotic genes, which represent the final step in pattern formation in the embryo.
Slide 6
Homeotic genes act last in the regulatory cascade. These genes further
refine the body plan of the developing embryo by determining the differences between
the segments – which segment will produce antennae, for example, or which will produce
pairs of legs. Mutations in homeotic genes can have astounding effects in organisms.
Certain mutations in fruit fly homeotic genes, for instance, lead to flies with a pair of legs
where their antennae should be, or flies with an extra pair of wings.
Slide 7
Looking at homeotic genes in more detail, we find that a key feature
common to all homeotic genes is the homeobox. The homeobox is a sequence of about
180 nucleotides in the DNA that codes for a polypeptide consisting of about 60 amino
acids. This polypeptide is called the homeodomain. The homeodomain is a protein that
recognizes and binds to specific sequences of DNA. Not surprisingly, the homeodomain
acts as a transcription factor, and controls the expression of many genes involved in finer
scale developmental processes. Although homeoboxes were originally found in homeotic
genes, they have since been found in other types of genes involved in development, such
as maternal effect genes.
Slide 8
Now let’s turn our attention to plants. In plants, organs such as leaves,
stems, and roots are determined by the interactions of groups of genes. The genes that
control the development of plant organs are called organ identity genes. Organ identity
genes are considered analogous to the homeotic genes of animals. In flowering plants,
organ identity genes interact to produce flowers with four parts – the sepals, petals,
stamens, and carpels. When plants flower, the development of these parts is determined
by three organ identity genes - a class A gene, a class B gene, and a class C gene. Similar
to the development we saw in the fruit fly, the products of these genes act as transcription
factors for numerous other genes involved in the development of each specific organ.
At first glance, it is apparent that there are more organs (four) than there are genes
(three). How do three genes produce four organs? As it turns out, the A, B, and C genes
work in tandem to determine which organ of the flower will form and in which position.
For example, if the A and B genes are expressed in a tissue, petals will form. If the B and
C genes are expressed in a tissue, stamens will form. If only the A or C genes are
expressed in a tissue, only sepals or carpels will form, respectively. On a molecular basis,
the gene products for the A, B, and C genes act in pairs as transcription factors. When
genes A and B are expressed in a tissue, proteins A and B combine to form a specific
type of transcription factor which activates the genes involved in petal formation. If only
gene A is expressed in a tissue, A proteins pair to form transcription factors specific to
genes involved in sepal formation. Mutation or manipulation of these three genes can
have interesting effects. If a plant lacks a functional class A gene, it will not be able to
produce sepals or petals. If a plant lacks the class B gene, it will only form sepals and
carpels.
Slide 9
It is also interesting to note that another gene, called the leafy gene, codes
for a transcription factor that activates genes A, B, and C. Plants without the leafy gene
are not able to make flowers at all, because they are not able to produce the transcription
factor necessary to activate genes A, B, and C. The leafy gene itself is regulated by the
activity of meristem identity genes. This again is another instance of a regulatory cascade.
Developmental genes are organized in a hierarchical manner. For each group of genes
involved in a stage of development, some of the protein products act directly in
development, while others act as transcription factors for the group of genes involved in
the next stage of development. As development proceeds, each group of genes expressed
results in further refinement of the organism.
Slide 10
Comparing the developmental pathways of different organisms provides
insight into the evolutionary history of development. There are many instances of
evolutionary conservation in developmental processes in diverse organisms. These
suggest a shared ancestry of these processes. The developmental genes controlling eye
formation, for instance, are very similar in distantly related animals, such as flies and
mammals. In Drosophila, a gene called eyeless codes for a transcription factor that binds
to and affects the expression of over 1500 genes involved in eye development. In mice, a
gene called Pax6 plays a similar role in eye development, coding for a transcription
factor affecting many other developmental genes. Although these two types of organisms
are fairly distantly related, the eyeless and Pax6 genes are extremely similar. In fact, if
the genes are exchanged between organisms, so that a fly develops with a mouse Pax6
gene, and a mouse with a fly eyeless gene, both the mouse and the fly will develop
normal, fully-functional eyes.
Research into homeoboxes has demonstrated that they occur in many, diverse types of
organisms. Generally, their sequence is not identical between different genes and
organisms, but it is usually very similar. In all cases, the homeodomain that they produce
acts as a transcription factor that affects other genes involved in development. The
prevalence of homeoboxes in developmental pathways, and their similarity between
many different types of organisms, suggests that they evolved from a common ancestor.
Most likely, homeoboxes have been conserved over time, with minor changes occurring
in the form of mutations. This conservation suggests that the differences between
organisms may be due to rather minor changes in a few genes. A change in a homeobox,
for instance, could change the homeodomain’s DNA binding properties, leading to a
difference in how much certain genes are expressed over others, resulting in phenotypic
differences.
The important concept to gain from these examples, and others like it, is that similar
genes often control similar developmental processes, even in very distantly related
organisms. This suggests that effective developmental processes evolved at some point in
the history of life, and were then conserved as they were passed on from generation to
generation. Over time, minor genetic differences began to accumulate due to mutations in
the DNA of individuals, leading to the larger phenotypic differences that we observe
today, such as the differences between species or broader taxa.