Chapter 19

1. Chapter 19 Comparative Genomics and the Evolution of Animal Diversity 04级生物学基地班200431060025 陈源

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

3. Topic 1 Most animal have essentially the same genes 1-1: different animals share essentially the same genes. The genetic conservation seen among vertebrates extends to the humble sea squirt. The genetic conservation seen among chordates appears to extend to other phyla.

4. 1-2 How does gene duplication give rise to biological diversity? There are two ways this can happen: 1 The conventional view is that an ancestral gene produces multiple genes via duplication ,and the new genes undergo mutation. 2 Duplication genes can generate diversity has been rather neglected until very recently.

5. Topic 2 Three ways gene expression is changed during evolution 1. A given pattern determining gene can itself be expressed in a new pattern. 2.The regulatory protein encoded by a pattern determining gene can acquire new functions. 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.

6. Topic 3 Experimental manipulations that alter animal morphology The first pattern determining gene was identified in Drosophila in the Morgan fly lab. A mutation called bxd causes a partial transformation of halteres into wings.

7. 3-1 Changes in Pax6 expression create Ectopic Eyes The most notorious pattern determining gene is Pax6, which control s eye development in most or all animals . Pax6 is normally expressed within developing eyes; but when misexpressed in the wrong tissres,Pax6 causes the development of extra eyes in those tissues. Evolutionary changes in the regulation of Pax6 expression have been more important for the creation of morphologically diverse eyes than have changes in Pax6 protein function.

8. 3-2 Changes in Antp expression transform Antennae into Legs A second Drosophila pattern determining gene, Antp, controls the development of the middle segment of the thorax, the mesothorax. Antp encodes a homeodomain regulatory protein that is normally expressed in the mesothorax of the developing embryo . But a dominant Antp mutation caused by a chromosome inversion brings the Antp protein coding sequence under the control of a foreign regulatory DNA that mediates gene expression in head tissues ,including the antennae.

9. 3-3 Importance of protein function: interconversion of ftz and Antp Pattern determining genes need not be expressed in different places to produce changes in morphology. A second mechanism for evolutionary diversity is changes in the sequence and function of the regulatory proteins encoded by pattern determining genes .

10. The Antp and Ftz proteins recognize distinct DNA-binding sites becarse they protein interactions are mediated by short peptide motifs that map outterapeptide sequence motif, YPWM.

11. Ftz-FtzF1 dimers recognize DNA sequences that are distinct from those bound by Antp-Exd dimers. As a result, Antp and Ftz regulate different target genes.

12. 3-4 Subtle changes in an enhancer sequence can produce new patterns of gene expression The third mechanism for evolutionary diversity is changes in the target enhancers that are regulated by pattern determining genes.

13. 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.

14. Dorsal functions synergistically with another transcription factor Twist to activate gene expression in the neurogenic ectoderm. There are no Twist binding sites in the native enhancer. A total of eight nucleotide substitutions are sufficient to create two Twist binding sites (CACATG). When combined with the two nucleotid substitutions that produce high-affinity Dorsal binding sites,the modified enhancer now directs a broad pattern of gene expression in both the mesoderm and neurogenic ectoderm.

15. A series of 2, 10, and 14 nucleotide substitutions produce a spectrm of Dorsal target enhancers which direct expression in the mesoderm, the mesoderm and neurogenic ectoderm, or just in the urogenic ectoderm. These observations suggest that enhancers can evolve quickly to create new patterns of gene expression.

16. 3-5 The misexpression of Ubx changes the morphology of the fruit fly New patterns of gene expression are produced by changing the Ubx expression pattern, the encoded regulatory protein, or its target enhancers. Antp is one of the genes that it regulates: Ubx represses Antp expression in the metathorax of developing embryos.

17. The expression of Ubx in the different tissues of the metathorax depends on regulatory sequences that encompass more than 80 kb of genomic DNA. The consequences of misexpressing a pattern determining gene can cause a dramatic change in morphology results.

18. 3-6 Changes in Ubx function modify the morphology of fruit fly embryos Ubx protein can function as a transcriptional repressor. The Ubx protein contains specific peptide sequences that recruit repression complexes. Ubx can be converted into an activator by fusing the Ubx DNA-binding domain to the potent activation domain from the viral VP-16 protein.

19. The protein sequences that mediate transcriptional repression map outside the Ubx homeodomain and are not present in the Ubx-VP16 fusion protein . The misexpression of the Ubx-VP16 fusion protein causes all of the segments to develop as mesothoracic segments. The Ubx-VP16 fusion protein produces the same phenotype as that obtained with Antp.

20. 3-7 Changes in Ubx target enhancers can alter patterns of gene expression The Ubx protein contains a homeodomain that mediates sequence-specific DNA binding, and it also contains a tetrapeptide motif (YPWM) that mediates interactions with Exd. Ubx binds DNA as a Ubx-Exd dimer.

21. Exd binds to a half-site with the core sequence, TGAT, Hox proteins such as Ybx bind an adjacent half-site with a diferent core consensus sequence, A-T-T/G-A/G. This obserbation raises the possibility that target enhancers regulated by one Hox protein can rapidly evolve into a target enhancer for a different Hox protein. So ,the altering the function or expression of the Ubxprotein or its target enhancers profoundly changes patterning in the Drosophila embryos and adults.

22. Topic 4 Morphological changes in crustaceans and insects The first two mechanisms, changes in the expression and function of pattern determining genes, can account for changes in limb morphology seen in certain crustaceans and insects; the third mechanism, changes in regulatory sequences, might provide an explanation for the different patterns of wing development in fruit flies and butterflies.

23. 4-1 Arthropods are remarkably diverse Arthropods embrace five groups: trilobites, hexapods, crustaceans, myriapods, and chelicerates. The success of the arthropods derives from their modular architecture. These organisms are composed of a series of repeating body segments that can be modified in seemingly limitless ways.

24. 4-2 changes in Ubx expression explain modifications in limbs among the crustaceans There are two different groups crustaceans, branchiopod and isopod. In branchiopods Scr expression is restricter to head regions where it helps promote the debelopment of feeding appendages,while Ubx is expressed in the thorax where it controls the development of swinning limbs.

25. In isopods, Scr expression is detected in both the head and the first thoracic segment(T1), and as a result, the swimming limb in T1 is transformed into a feeding appendage. This posterior expansion of Scr was made possible by the loss of Ubx expression in T1 since Ubx normally represses Scr expression.

26. During the divergence of branchiopods and isopods, the Ubx regulatory sequence changed in isopods. As a result of this change, Ubx expression was eliminated in the first thoracic segments, and restricted to segments T2-T8. In Artemia, these head genes are kept off in all 11thoracic segments, but in isopods the head genes can be expressed in the T1 segment due to the loss of the Ubx repressor.

27. Expression of the Scr gene is restricted to head regions of branchiopods, but is expressed in T1of isopods. The expression of Scr in T1 causes maxillipeds to develop in place of normal swimming limbs.

28. 4-3 Why insects lack abdominal limbs? The loss of abdominal limbs in insects is due to functional changes in the Ubx regulatory protein. In insects, Ubx and abd-A repress the expression of a critical gene that is required for the development of limbs, call Dll. Although Ubx is expressed in metathorax, it does not interfere with the expression of Dll in that segment, because Ubx is not expressed in the developing T3 legs until after the time when Dll is activated, as a result, Ubx does not interfere with limb development in T3.

29. The misexpression of Ubx throughout all of the tissues of the presumptive thorax in transgenic Drosophila embryos suppresses limb development due to the repression of Dll. The misexpression of the crustacean Ubx protein in transgenic flies does not interfere with Dll gene expression and the formation of thoracic limbs.

30. 4-4 modification of flight limbs might arise from the evolution of regulatory DNA sequences Changes in the Ubx expression pattern appear to be responsible for the transformation of swimming limbs into maxillipeds in crustaceans.

31. Ubx in crustaceans, the C-terminal antirepression peptide blocks the activity of the N-terminal repression domain. Ubxin insects ,the C-terminal antirepression peptide was lost throught mutation.

32. Two possibilities: First, the Ubx protein is functionally distinct in flies and butterfiles. Second, each of the approximately five to ten target genes that are repressed by Ubx in Drosophila have evolved changes in their regulatory DNAs so that they are no longer repredded by Ubx in butterflies.

33. The Ubx repressor is expressed in the halters of dipterans and hindwings of lepidopterans. Different target fenes contain Ubx repressor sites in dipterans. These habe been lost in lepidopterans. An implication of the preceding arguments is that evolutionary changes regulatory DNAs.

34. Topic 5 Genome evolution and human origins The genomes of mice and humans have been sequenced and assembled, and their comparison should shed light on our own human origins.

35. 5-1 Humans contain surprisingly few genes The human genome contains only 25000-30000 protein coding genes. Before the human genome was sequenced, there were popular estimates for 100000 protein coding genes. Organismal complexity is not correlated with gene number, but instead depends on the number of gene expression patterns.

36. 5-2 The human genome is very similar to that of the mouse and virtually identical to the chimp Mice and humans contain roughly the same number of genes, approximately 80% of these genes possess a clear and unique one-to-one sequence alignment with one another between the two species. Most of the remaining 20% of the genes in mice and humans differ by virtue of lineage-specific gene duplication events.

37. The chimp and human genomes are even more highly conserved, they vary by an average of just 2% sequence divergence. The regulatory DNA evolve more rapidly than proteins.

38. 5-3 the evolutionary origins of human speech Speech depends on the precise coordination of the small muscles in our larynx and mouth. Reduced levels of a regulatory protein called FOXP2 cause severe defects in speech. Changes in the expression pattern or changes in FOXP2 target genes might be responsible for the ability of FOXP2 to promote speech in humans.

39. 5-4 How FOXP2 fosters speech in humans Changes in the FOXP2 expression pattern, changes in its amino acid sequence, and changes in FOXP2 target fenes might explain its emergence as an important mediator of human speech. Some might encode neurotransmitters or other critical signals that are expressed within the developing larynx. FOXP2 is just one example of a regulatory fene that underlies human speech.

40. A scenario for the evolution of speech in humans. A hypothetical regulatory protein is expressed in the neocortex of both chimps and humans. The human gene is strongly expressed at the critical time in the development of the speech center and activates all three hypothetical target genes in the neocortex, these target gene might encode neurotransmitters important for the formation of the speech center.

41. 5-5 The future of comparative genome analysis There is a glaring limitation in our ability to infer the function of regulatory DNA from simple sequence inspection . In the future it might also be possible to identify changes in the expression profiles of homologous genes.

42. Summary The same concept of differential gene expression can explain the evolution of animal diversity. Changes in gene expression during evolution depend on altering the activities of a special class of regulatory genes, called pattern determining genes. There are three major strategies for altering the activities of pattern determining genes. We are fast entering a golden era of comparative genome analysis.

43. The End Thank you!