Chaper 19 Comparative Genomics and the Evolution of Animal Diversity

1. Chaper 19Comparative Genomics and the Evolution of Animal Diversity 2004生物科学 倪向敏200431060142

2. outline • Topic 1: Most animals have essentially the same genes • Topic 2: Three ways gene expression is changed during evolution • Topic 3: Experimental manipulations that alter animal morphology • Topic 4: Morphological changes in crustaceans and insects • Topic 5: Genome evolution and human origins

3. Charles Darwin : all animals arose from a common ancestor! Over the course of many millions of years of evolution, a flat worm lived in burrows beneath the ancient oceans spawned the remarkable diversity we now see among modern animals.

4. Figure 19-1 summary of phyla • There are 25 different animal phyla and most fall into three major groups: lophotrochozoans , ecdysozoans, and deuterostomes.

5. Topic 1 : Most animals have essentially the same genes

6. Comparison of the currently available genomes reveals one particularly striking feature : different animals share essentially the same genes. Pufferfish , mice and human genomes comparison: about every human genes has a clear counterpart in the mouse genome ; more than three quarters of human and pufferfish genes can be unambiguously aligned.

7. Figure 19-2 Phylogeny of assembled genomes The relationship among those animals whose genomes have been sequenced to date

8. The genetic conservation seen among vertebrates extends to the humble sea squirt. • It contains half the number of genes present in vertebrates; • Nearly two-thirds of the protein coding genes contain a clear recognizable counterpart in vertebrates; • The increase in gene number seen in vertebrates is due to the duplication of genes present in the sea squirt. (for example, EGF genes )

9. Figure 19-3 phylogenetic tree showing gene duplication of the fibroblast growth factor genes (EFG) Cioca EFGs are shown in orange ,whereas vertebrate are shown in orange. Branchless is an EFG found in drosophila.

10. How does gene duplication give rise to biological diversity? Two ways : • Conventional view --- the coding regions of the new duplication genes undergo mutation. These mutant genes encode related proteins with slightly different activities. • Recent view --- duplicated genes contain new regulatory DNA sequences. This allows different copies of the gene to be expressed in different patterns within the developing organism.

11. The high degree of conservation of the genes found in different animals has recently focused the changes in gene expression as a general mechanism in generating evolutionary diversity. how?

12. Topic 2 Three ways gene expression is changed during evolution

13. Pattern determining genes: a class of regulatory genes • Changes of the activities and expression patterns of these genes during evolution seem to cause significant changes in animal morphology. • Distinguishing characteristic---cause correct structures to develop.

14. Three major strategies for altering the activities of pattern determining genes • 1.Agiven pattern determining gene can be expressed in a new pattern. This will cause those genes whose expression it controls to acquire new patterns of expression. • 2.Theregulatory protein encoded by a pattern determining gene can acquire new functions (for example, a transcriptional activation domain can be converted into a repression domain). • 3.Target genes of a given pattern determining gene can acquire new regulatory DNA sequences, and thus come under the control of a different regulatory gene.

15. Figure 19-4 summary of the three strategies for altering the foles of pattern determining genes Proteins acquire new functions through mutation. Altering the expression of the pattern determining gene. Different garget genes are regulated due to changes in enhancer sequences

16. Topic 3 Experimental manipulation that alter animal morphology

17. Abnormal morphologies are obtained through each of the three mechanisms: 1.altering the expression 2.altering the function 3.altering the targets of the pattern determining genes

18. Changes in Pax6 expression create ectopic eyes Pax6 • pattern determining gene which controls eye development in most or all animals. • is normally expressed within developing eyes. • misexpressed in the wrong tissues causes the development of extra eyes in those tissues. • expression pattern changes are probably for some of morphological diversity (positioning of eyes) among the eyes of different animals.

19. Figure 19-5 misexpression of Pox6 and eye formation in Drosophila

20. Evolutionary changes in regulation of Pax6 expression have been more important for the creation of morphologically diverse eyes than have changes in Pax6 protein function. Pax6 genes from other animals also produce ectopic eyes when misexoressed in drosophila.

21. Fruit flies were engineered to misexpress the squid Pax6 gene.Extra eyes were obtained in the wings and legs .

22. Changes in Antp expression transform antennae into legs Antp: • a second Drosophila pattern determining gene • controls the development of the middle segment of the thorax, the mesothorax. • encodes a homeodomain regulatory protein that is normally expressed in the mesothorax of the developing embryo. • not expressed in the developing head tissues.

23. Figure 19-6 a dominant mutation in the Antp gene results in the hemeotic transformation of antennae into legs When misexpressed in the head ,Antp causes a striking change in morphology: legs develop instead of antennae.

24. Importance of protein function: interconversion of ftzand Antp Two related pattern determining genes in Drosophila : the segmentation gene---ftz the homeotic gene---Antp These genes are linked and arose from an ancient duplication event. The two encoded proteins are related and contain very similar DNA-binding domains (homeodomains)

25. The Antp and Ftz proteins recognize distinct DNA-binding sites because they form heterodimers with different “partner” proteins • Antpcontains a tetrapeptide sequence motif, YPWM, which mediates interactions with a ubiquitous regulatory protein called Exd (Extradenticle) . • Ftzcontains s pentapeptide sequence, LRALL, which mediates interactions with a different ubupuitous regulatory protein ,FtzF1

26. Ftz-FtzF1 dimers recognize DNA sequences that are distinct from those bound by Antp-Exd dimers. Antp and Ftz regulate different target genes. Figure 19-7 Duplication of ancestral gene leading to Antp and ftz

27. Subtle changes in an enhancer sequence can produce new patterns of gene expression • Changes in the target enhancers that are regulated by pattern determining genes for evolutionary diversity can be nicely illustrated by the Dorsal regulatory gradient in the early fly enbryo.

28. Binding affinities of Dorsal recognition sequences produce distinct patterns of gene expression. • Target enhancers with low-affinityDorsal binding sites are expressed in the mesoderm, where there are high levels of the Dorsal gradient. • Target enhancers withhigh-affinitysites are expressed in the neurogenic ectoderm, where there are intermediate and low levels of the gradient.

29. The principle that changes in enhancers can rapidly evolve new patterns of gene expression stems from the experimental manipulation of a 200 bp tissue specific enhancer that is activated only in the mesoderm. The enhancer contains two low-affinity Dorsal binding sites and is activated by high levels of Dorsal gradient in ventral regions (the future mesoderm).

30. Single nucleotide substitutions that convert each site into an optimal Dorsal binding site cause the modified enhancer to be activated in a broader pattern. • A total of eight nucleotide substitutions (sufficient to create two Twist binding sites) combined with the two nucleotide substitutions that produce high-affinity Dorsal binding sites caused the modified enhancer to direct a broad pattern of gene expression in both the mesoderm and neurogenic. • A few additional nucleotide changes create binding sites for a zinc finger repressor---Snail. The modified enhancer, containing optimal Dorsal sites, Twist activator sites, and Snail repressor sites , is expressed only in the neyrogenic ectoderm where there are low levels of the Dorsal gradient.

31. Figure 19-8 regulation of transgene expression in the early Drosophila embryo

32. Altogether, a series of 2,10, 14 nucleotide substitutions produce a spectrum of Dorsal target enhancers which direct expression in the mesoderm, the mesoderm and neurogenic ectoderm, or just in the neurogenic ectoderm. suggest that enhancers can evolve quickly to create new patterns of gene expression.

33. Ubx • a drosophila pattern determining gene. • It’s analysis illustrates all three principles of evolutionary changes. • New patterns of gene expression are produced by: 1.Changing the Ubx expression pattern 2.Changing the encoded regulatory protein 3.Changing its target enhancer

34. The misexpression of Ubx changes the morphology of the fruit fly Ubx: • encodes a homeodomain regulatory protein that controls the development of the third thoracic segment , the metathorax. • specifically represses the expression of genes that are required for the development of the second thoracic segment, or mesothorax.

35. Antp is one of the genes that Ubx regulated: Ubx represses Antp expression in the metathorax and restricts its expression to the mesothorax of developing embryos. • Mutants that lack the Ubx repressor exhibit an abnormal pattern of Antp expression. The gene is not only expressed within its normal site of action in the developing mesothrax, but it is also misexpressed in the developing metathorax. This misexpression of Antp causes a transformation of the metathoraxinto a duplicated mesothorax.

36. A normalfly contains a pair of prominent wings and a set of halteres. A mutant that is homozygous for a weak mutation in the Ubx gene has two pairs of wings and no halteres. Figure 19-9 Ubx mutants cause the transformation of the metathorax into a duplicated mesothorax.

37. The expression of Ubx in the different tissues of the mitathorax depends on regulatory sequences that encompass more than 80 kb of genomic DNA. • A mutants Cbx (Contrabithorax) disrupts this Ubx regulatory DNA without changing the Ubx protein coding region. • Causes Ubx to be misexpressed in the mesothorax, in addition to its normal site of expression in the metathorax. • The mesothorax is transformed into a duplicated copy of the normal metathorax.

38. The wings are transformed into halteres. Figure 19-10 misexpression of Ubx in the mesothorax results in the loss of wings.

39. Changes in Ubx function modify the morphology of fruit fly The conversion of Ubx into a transcriptional activator causes it to function like Antp and promote the development of the mesothorax. illustrates how changes in the function of a pattern determining regulatory protein can alter morphology.

40. Ubx nromally functions as a repressor. • The Ubx protein contains specific peptide sequences that recruit repression complex. • One such peptide is composed of a stretch of alanine residues---alanine rich repression domains.

41. The misexpressin of Antp causes all of the head and thoracic segments of the embryo to develop as duplicated mesothoracic segments, all the thoracic segments contain denticle patterns that look like the one normally present only on the mesothorax. • The misexpression of Ubx causes all three thoracic segments to develop denticle patterns typical of the normal first adominal segment.

42. Fuse the Ubx DNA-binding domain (homeodomain) to the potent activation domain from the viral VP16 protein. • Ubx is converted into an activator. • The misexpression of the Ubx-VP16fused protein causes all of the segment to develop as mesothoracic segments ,not metathoracic segments as seen when the normal Ubx protein is misexpressed in engineered embryos. • The Ubx-VP16 protein produces the same phenotype as that obtained with Antp.

43. Normal embryo • The misexpression of Ubx • The misexpression of a Ubx-VP16 fused protein . • The misexpression of the normal Antp protein. Figure 19-11 changing the regulatory activities of the Ubx protein

44. Changes in Ubx target enhancers can alter patterns of gene expression • The Ubx protein contains a homeodomain that mediates sequence-specific DNA binding. • Ubs also contains a tetrapeptide motif [YPWM] that mediates interactions with Exd. • Ubx binds DNA as a Ubx-Exd dimer.

45. Many homeotic regulatory proteins interact with Exd and bind a composite Exs-Hox recognition sequence: • Exd binds to a half-site with the core sequence, TGAT. • Hox proteins such as Ubx binds an adjacent half-site with a different core consensus sequence, A-T-T/G-A/G.

46. The two half-sites are often separated by two nucleotides. determine which Exd-Hox dimer can bind: • Exd-Ubx dimers prefer T-T in the central position. • Exd-Labial dimers prefer G-G central residues. Raise the possibility the target enhancer regulated by one Hox protein can rapidly evolve into a target enhancer for a different Hox protein.

47. Figure 19-12 interconversion of Labial and Ubx biding sites The Hox subunit makes additional contacts with the central two nucleotides (NN). The exact sequence of these residues strongly influences spicificity.

48. Topic 4 Morphological changes in crustaceans and insects

49. Arthropods are remarkably diverse Arthropods embrace five groups: 1.trilobites (三叶虫 sadly extinct) 2.hexapods (such as insects) 3.crustaceans (shrimp, lobsters, crabs and so on) 4.myriapods (centipedes and millipedes) 5.chelicerates (horseshoe crabs spiders and scorpions)

50. The success of the arthropods derives ,in part, from their modular architecture. • They are composed of a series of repeating body segments that can be modified in seemly limitless ways. • Some segments carry wings, whereas others have antennae, legs, jaws, of specialized mating devices. • We know more about the evolutionary processes responsible for the diversification of arthropods than for any other group of animals.