Lecture 08

Question 1

Genomics and developmental biology

a. Discuss The genome sequence-static data set

Answer 1

Genome sequence – static data set
a. yet, implementation in cells is dynamic, and thus, genomes contain developmental programmes governing gene expression patterns at
different life stages, differentiated tissues + reactions and responses to environmental stimuli

Question 2

Discuss examples of organisms with different body plans but similar developmental toolkits(2)(3)

Answer 2

Different body plans, but similar developmental toolkits

a. HOX genes – responsible for anterior–posterior (head-to-tail) patterning in the body plans of flies, humans and nematode (Fig. 1.17)

b. PAX6 in humans is required for proper eye development, but if expressed in Drosophila can transform embryonic wing tissue to an ectopic eye
* despite huge diff’s in gross eye anatomy in vertebrates, insects and
octopus, visual systems arose from a common ancestor
* evidence from mol. str. of rhodopsins + architect. of neural pathways

Question 3

What do full-genome sequences permit?

• This makes it possible to?(1)
• What does it illuminate?(1)

Answer 3

Full-genome sequences permit identification of similarities and differences in developmental processes during evolution (‘evo-devo’)

• possible to identify developmental gene homologues across different phyla
• illuminate phylogenetic relationships and ,thus, extrapolate (to molecular level) classical embryology and taxonomy

Question 4

Discuss the characteristics of Cnidaria(4)

Answer 4

Cnidaria
* Phylum cnidaria: ~10,000 species of aquatic animals (e.g. sea anemones and jellyfish)
* Buddenbrockia plumatellae; a worm that doesn’t resemble cnidarians, but rather nematodes
* Sequence alignments of 129 proteins – B. plumatellae is a cnidarian
* extends the body plan observed for cnidaria, requiring investigation of unsuspected aspects of the
developmental pathways in this species

Question 5

Discuss HOX genes(2)

Answer 5

HOX genes

• organisms with bilateral symmetry encode these DNA-binding proteins with anterior-posterior expression patterns – set out the body plan
• expression differ within and among species – chr order, dev. temporal expression + order of action in body; diff no. of clusters -> conservation of dev. toolkit in different body plans

Question 6

Discuss DNA methylases(3)

Answer 6

DNA methylases
* signals for transcription control in vertebrate dev. and tissue differentiation

• no methylation in invertebrates (e.g. C. elegans); but D. melanogaster has some genes and honeybee has all genes and its genome gets methylated
• distribution of DNA methylases -> diversification of dev. toolkit in similar body plan

Question 7

Protein evolution: divergence of sequences and structures within and among species

a. What are the mechanisms of protein evolution?(2)
b. How do essential proteins evolve without depriving cells of their functions?(1)(3)

Answer 7

Mechanisms of protein evolution – two major sources

a. mutations – at the DNA level (substitutions or indels)
* substitutions  no change vs. conservative vs. severe change
* indels  3 bp vs. 1 bp or 2 bp or 4 bp or 5 bp, etc
a. domain ‘mix and match’ – safe way to generate diversity; often, domains do not retain their functions

b.How do essential proteins evolve without depriving cells of their functions?
* gene duplication, followed by divergence – for example, globins (see Box 1.15)
* multi-function proteins
- depending on the cell’s requirements, evolution would then optimize
the protein for one or another function, if not retain both
- prokaryotes – import plasmids (i.e. HGT) with desired functions (e.g.
antibiotic resistance)

Question 8

Discuss globins(3)

Answer 8

Globins
* within each cluster are more closely related
than between clusters
* others (myo-, neuro- and cytoglobin) are
distantly related
* divergence at molecular level correlates
with species level divergence (similar to
classical taxonomical methods)

Question 9

a. Discuss sequence alignment(4)

b. Discuss the phylogenetic tree(2)

Answer 9

a.Sequence alignment
* color-coding of amino
acids
* cap vs small letter amino
acids
* alignment gaps
* distantly-related
sequence

b. Phylogenetic tree
* sequence divergence, not
species
* distantly-related
sequence still the same!