Download Biol/Chem 473 See web site for Reading Assignment for next week`s

Biol/Chem 473
See web site for Reading Assignment for next week’s exam:
• Link to paper
• Study Questions
• At least 25 pts of the next exam will be on this paper
Reading Assignments for next few lectures:
Alberts
Chapter 21: pg. 1190-1198 on HOX genes
Chapter 7: pg 425-427 (ey gene); 459-461 (gene duplication)
More Seminar Opportunities:
Dr. Carolyn Bertozzi from UC Berkeley
Friday 5/16 10-11 am Biophys class
Chemical Approaches to Glycomics
Friday 5/16 5-6pm Plenary lecture
Sulfation Pathways in Inflammation and in Mycobacterial Infection
animals shown: anomalocaris and hallucigenia
1
The Cambrian Explosion - 550 MYA
THE BIG BANG OF ANIMAL EVOLUTION
v Cambrian explosion was characterized by the sudden and roughly simultaneous
appearance of many diverse animal forms about 550 MYA.
vNo other period in the history of life can match this remarkable burst of
evolutionary creativity
v Marks the appearance of abundant life as recorded by an abundance of marine
fossil life
v Marks the appearance of invertebrates with mineralized (calcium carbonate)
skeletons [on formerly soft-bodied organisms]
hallucigenia and Opabinia
2
vNo other period in the history of life can match this remarkable burst of
evolutionary creativity
Opabinia
(lower right)
has five
eyestalks!
3
The Cambrian Explosion: Before and After
What major adaptive features were in place before the Cambrian explosion?
• Before and after the event all life lived in the oceans.
• The major adaptive features that were already present:
1. eukaryotic cell
2. sexual reproduction
3. multi-cellular organisms with soft bodies
Ì What were the major evolutionary adaptations that arose during the event?
v The body plans of all major extant animal phyla
Animals appeared in the fossil record with a clearly distinguished front end
and back end
Many different lineages acquired complex anatomies and hard parts (the
exoskeleton) at the same time
• the jellyfish and radial symmetry [cnidarians]
• segmentation [annelids, arthropods]
• calcareous shells [mollusca]
• the exoskeleton [arthropodS]
• the notochord [chordates]
4
What factors triggered the Cambrian explosion?
The Cambrian record of life is in sharp contrast with that of the preceeding eons
The Cambrian appearance of fossils representing diverse phyla has inspired
hypotheses about possible genetic or environmental catalysts of early animal
evolution:
The genetic toolkit hypothesis
o The Cambrian explosion was ignited by the evolution of a “modern genetic
toolkit” that was complex enough to facilitate elaborate diversification of
body plans
The environment/ecological hypothesis
o The genetic toolkit was in place well before the Cambrian radiation (that is
predated the Paleozoic Era)
o The Cambrian explosion was triggered by environmental perturbations and
amplified by ecological interactions within reorganized ecosystems
What is meant by the Genetic Toolkit?
Housekeeping genes: genes that encode proteins that function in essential
processes in all cells in the body
Such as?
Roomkeeping genes: Other genes encode proteins that carry out specialized
functions in particular cells or issues
Such as?
The genetic toolkit: genes that govern the construction of the house
Or in other words whose protein products determine the overall body plan and the
number, identity and pattern of body parts
How to identify such genes?
What are the Old and new paradigms?
5
Critical Features of the Toolkit
OR What we know so far
1. The toolkit is composed of a small fraction of all genes
2. Most toolkit genes encode transcription factors or components of signaling
pathways and act directly or indirectly to control the expression of other genes
3. The spatial expression of toolkit genes is often closely correlated with the
region of the animal in which the gene functions
4. Toolkit genes can be classified according to the phenotypes caused by their
mutation:
o body axis specification
o formation and identity of spatial fields
o specification of a specific organ (such as the eye)
5. Many toolkit genes are widely conserved among different animal phyla
Many members of the genetic toolkit are homeobox or zinc finger genes
Genome-wide analysis of DNA-binding motifs found in eukaryotic transcription
factors
6
The homeobox family: a transcription factor family
♦ homeodomain is a ~60 amino acid sequence containing many basic residues
♦ forms a helix-turn-helix motif that binds specific sequences in DNA
♦ the homeodomain is coded for by the homeobox region of the gene
Helix-3 contacts the major groove.
The specific amino acid sequence of helix-3 determines the DNA binding
specificity of the homeodomain protein
7
Homeodomains are highly similar 60 amino acid regions of proteins made by all
homeobox gene.. Deviations from the consensus are shown for four fly (top line)
and mouse (bottom line) homeodomain proteins. A dash means the sequence
matches that of the consensus.
8
How do we know that homeobox genes are part of the “genetic
toolkit” [as defined above]?
How do we know that this class of genes is often involved in
developmental events?
How do we know that they are transcriptional regulators?
9
Homeotic genes
♦ homeobox originally named for Drosophila homeotic genes: mutations in these
genes transform one body part into another
♦ genes with a homeobox often are involved as developmental regulators, but
possession of a homeodomain does not guarantee a role in development
♦ not all mutants are homeotic
bithorax mutant phenotype
Homeotic genes are part of a hierarchy of regulators that define spatial
location in the developing fly embryo
If building an embryo, what are the first decisions that need to be made?
10
Based on extensive analysis of developmental mutation in flies, three general class
of early developmental regulatory genes have been defined:
AP/DV Genes: define embryonic axes
â regulate expression of
Segmentation Genes: define segment boundaries and polarity
â regulate expression of each other and
Homeotic Genes (segment identity along the AP axis)
â regulate expression of each other and
Genes necessary for assembling the specialized structures and tissue in each
segment
AP/DV genes: homeobox genes, zinc fingers, signal transduction genes
Segmentation genes: zinc fingers, homeobox genes
A subset of
homeobox genes
are called the HOX
genes
o found in
linked clusters
and only in
animals
o role in
specifying
location along
the AP axis
11
o Color coding represents the segments and structures in the embryo and adult
that are affected by mutations in the various HOX genes
o The Drosophila homeobox genes are shown in their actual linkage order.
o What is interesting about this arrangement?
Eight HOX genes regulate the identify of regions within the adult and the embryo
12
13
Remarkable observations:
1. Homeobox-containing genes have been found in all metazoan organisms
examined as well as in yeast and plants
2. In most (all) metazoans some of the homeobox genes are organized into gene
clusters that are colinear with the Drosophila BX-C and ANT-C gene clusters.
Homeobox “equivalents” very similar homeodomain sequences (see next
figure)
3. As in Drosophila, the relative order of a gene within each vertebrate HOX
complex is correlated with its spatial expression along the anteroposterior body
axis
14
Homeodomain Consensus sequence at top of figure
For each box: first line is a fly homeodomain and the second line is a mouse
homeodomain. In each box, the homeodomains are more closely related in
sequence to each other than they are to other homodomains from the same
organism
15
In the mouse embryo, four complexes of HOX genes (39 genes in all) occur on four
different chromosomes. Not every gene is represented in every complex. The HOX
genes are expressed in distinct domains along the AP axis
16
As in Drosophila, the relative order of a gene within each vertebrate HOX complex
is correlated with its spatial expression along the anteroposterior body axis
Photomicrographs showing the mRNA expression patterns of three mouse Hox
genes in the vertebral column of a sectioned 12.5 day old embryo.
Note that the anterior limit of each of the expression patterns is different
How do we know that these variations in expression pattern have any meaning?
How can we directly address HOX gene function in vertebrates?
17
Many toolkit genes are widely conserved
among different animal phyla
18
Many toolkit genes are widely conserved
among different animal phyla
The striking correspondence between the gene clusters in flies and mammals and
other animals suggests that they represent the descendants of an ancestral cluster
of homeobox genes already present in the common ancestor of insects and
vertebrates and other bilateral organisms
…………….which would have predated the Cambrian explosion
Two view of an
ancestor: the
ancestral bilateral
animal may have
been relatively
simple (top) but
genetic evidence
suggests that it
could have been
more
sophisticated
(bottom)
19
So what did the genetic toolkit look like for the last common ancestor of all
bilaterally symmetric organisms?
What other genes are shared by all descendants
Rebuilding Urbilateria: the hypothetical last common ancestor of all bilaterans
The pax-6 gene is the subject of the assigned paper
20
OPTional stuff if you are interested:
Hox genes and the evolution of tetrapod axial identities
differences in the axial organization of tetrapods are reflected in shifts in Hox gene
expression domains between animals.
square = vertebrae circle = somites
green = cervical purple = thoracic
o In mammals and birds, which have distinct cervical (green) and thoracic
(purple) axial regions, the anterior boundary of expression of the Hoxc6
gene lies at the cervical-thoracic transition
o the anterior boundary of the Hox c8 gene lies within the thorax
o the Hoxa,b,c9 boundary lies at the thoracic-lumbar transition
the vertebral column of snakes does not have a clear cervical-thoracic boundary.
In the python, the Hoxc6 and Hoxc8 genes have a more anterior expression
boundary, reflecting the expanded thoracic vertebrae in the snake body plan.
Within the domain of the Hoxc6 and Hoxc8 and expression, all of the python
vertebrae have ribs, indicating thoracic identity. The loss of the snakes neck and
expansion of its rib-bearing vertebrae are correlated with the anterior shift in the
expression of these two genes
21
Recall that the HOX genes regulate the transcription of each other and of
downstream genes involved in tissue/organ “assembly”
Note mutations in the homeobox gene UBX affect the third thoracic segment and
first abdominal segment.
“Primitive” state: four wings
• The homeodomain protein UBX is a transcriptional repressor
• Evolutionary conversion of hindwings to halteres in flies probably involved
the acquisition of UBX binding (cis-acting) sites in the regulatory regions of
genes required for outgrowth of wing tissue (such as the gene wingless).
Expression of UBX protein in the third thoracic segment in flies then
repressed wing development.
• In butterflies, UBX is expressed in the third thoracic segment, but it does not
repress wing outgrowth, possibly because there are no UBX-binding sites in
the cis-regulatory DNA of the butterfly wingless (and other) genes.
22
The homeobox gene UBX is expressed in the third thoracic segment and represses
wing development in the fly
Interested in this topic?-- see this 2-page Nature paper:
http://fire.biol.wwu.edu/trent/trent/Nature2.21.02.pdf
Evolution through changes in Hox target genes. Among the insects, dipterans (such
as Drosophila,top) have rudimentary wings, called halteres, in place of hindwings.
Ubx represses growth in the halteres,suppressing wing development. In contrast,
lepidopterans (such as moths, bottom) have well-developedhindwings. Ubx does
not suppress growth in lepidopteran hindwings, and it has been proposed that the
cis-regulatory sequences associated with these genes lack binding sites for the Ubx
repressor. In butterflies,Ubx primarily regulates genes that determine
characteristics of the hind- and forewings, such as those involved in determining
shape and colour.
23