Chapter 19Chapter 19Comparative Genomics anComparative Genomics and the Evolution of Animal d the Evolution of Animal

Diversity Diversity 0404 级生物学基地班级生物学基地班 200431060025200431060025

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OutlineOutline

1:Most animal have essentially the same genes1:Most animal have essentially the same genes

2:Three ways expression is changed during 2:Three ways expression is changed during evolutionevolution

3:Experimental manipulations that alter animal 3:Experimental manipulations that alter animal

MorphologyMorphology

4:Morphological changes in crustaceans and 4:Morphological changes in crustaceans and insectsinsects

5:Genome evolution and human origins5:Genome evolution and human origins

Topic 1 Most animal have essentially Topic 1 Most animal have essentially

the same genesthe same genes1-1: different 1-1: different animalsanimals share essentially the share essentially the

same genes.same genes.

The genetic conservation seen among vertebrates The genetic conservation seen among vertebrates extends to the humble sea squirt.extends to the humble sea squirt.

The genetic conservation seen among chordates The genetic conservation seen among chordates appears to extend to other phyla.appears to extend to other phyla.

1-2 How does gene duplication give 1-2 How does gene duplication give rise to biological diversity?rise to biological diversity?

There are two ways this can happen:There are two ways this can happen:

1 The conventional view is that an ancestral gene 1 The conventional view is that an ancestral gene produces multiple genes via duplication ,and produces multiple genes via duplication ,and the new genes undergo mutation.the new genes undergo mutation.

2 Duplication genes can generate diversity has 2 Duplication genes can generate diversity has been rather neglected until very recently.been rather neglected until very recently.

Topic 2 Three ways gene expression Topic 2 Three ways gene expression is changed during evolutionis changed during evolution

1. A given pattern determining gene can itself be 1. A given pattern determining gene can itself be expressed in a new pattern.expressed in a new pattern.

2.The regulatory protein encoded by a pattern 2.The regulatory protein encoded by a pattern determining gene can acquire new functions.determining gene can acquire new functions.

3.Target genes of a given pattern determining 3.Target genes of a given pattern determining gene can acquire new regulatory DNA gene can acquire new regulatory DNA sequences, and thus come under the control of sequences, and thus come under the control of a different regulatory gene.a different regulatory gene.

Topic 3 Experimental manipulations Topic 3 Experimental manipulations that alter animal morphologythat alter animal morphology

The first pattern determining gene was identified The first pattern determining gene was identified in Drosophila in the Morgan fly lab. in Drosophila in the Morgan fly lab.

A mutation called bxd causes a partial transformA mutation called bxd causes a partial transformation of halteres into wings.ation of halteres into wings.

3-1 Changes in Pax6 expression crea3-1 Changes in Pax6 expression create Ectopic Eyeste Ectopic Eyes

The most notorious pattern determining gene is Pax6, wThe most notorious pattern determining gene is Pax6, which control s eye development in most or all animals .hich control s eye development in most or all animals .

Pax6 is normally expressed within developing eyes; but Pax6 is normally expressed within developing eyes; but when misexpressed in the wrong tissres,Pax6 causes twhen misexpressed in the wrong tissres,Pax6 causes the development of extra eyes in those tissues.he development of extra eyes in those tissues.

Evolutionary changes in the regulation of Pax6 expressiEvolutionary changes in the regulation of Pax6 expression have been more important for the creation of moron have been more important for the creation of morphologically diverse eyes than have changes in Pax6 phologically diverse eyes than have changes in Pax6 protein function.protein function.

3-2 Changes in Antp expression tran3-2 Changes in Antp expression transform Antennae into Legssform Antennae into Legs

A second Drosophila pattern determining gene, Antp, coA second Drosophila pattern determining gene, Antp, controls the development of the middle segment of the tntrols the development of the middle segment of the thorax, the mesothorax.horax, the mesothorax.

Antp encodes a homeodomain regulatory protein that is Antp encodes a homeodomain regulatory protein that is normally expressed in the mesothorax of the developinormally expressed in the mesothorax of the developing embryo .ng embryo .

But a dominant Antp mutation caused by a chromosome But a dominant Antp mutation caused by a chromosome inversion brings the Antp protein coding sequence uninversion brings the Antp protein coding sequence under the control of a foreign regulatory DNA that medider the control of a foreign regulatory DNA that mediates gene expression in head tissues ,including the antates gene expression in head tissues ,including the antennae.ennae.

3-3 Importance of protein function: i3-3 Importance of protein function: interconversion of ftz and Antpnterconversion of ftz and Antp

Pattern determining genes need not be expressed Pattern determining genes need not be expressed in different places to produce changes in in different places to produce changes in morphology. morphology.

A second mechanism for evolutionary diversity A second mechanism for evolutionary diversity is changes in the sequence and function of the is changes in the sequence and function of the regulatory proteins encoded by pattern regulatory proteins encoded by pattern determining genes .determining genes .

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

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

3-4 Subtle changes in an enhancer 3-4 Subtle changes in an enhancer sequence can produce new patterns sequence can produce new patterns

of gene expression of gene expression The third mechanism for evolutionary diversity The third mechanism for evolutionary diversity

is changes in the target enhancers that are is changes in the target enhancers that are regulated by pattern determining genes.regulated by pattern determining genes.

The principle that changes in enhancers can rapiThe principle that changes in enhancers can rapidly evolve new patterns of gene expression stedly evolve new patterns of gene expression stems from the experimental manipulation of a 20ms from the experimental manipulation of a 200 bp tissue specific enhancer that is activated o0 bp tissue specific enhancer that is activated only in the mesoderm.nly in the mesoderm.

Dorsal functions synergistically with another transcriptiDorsal functions synergistically with another transcription factor Twist to activate gene expression in the neuon factor Twist to activate gene expression in the neurogenic ectoderm.rogenic ectoderm.

There are no Twist binding sites in the native enhancer.There are no Twist binding sites in the native enhancer.

A total of eight nucleotide substitutions are sufficient to A total of eight nucleotide substitutions are sufficient to create two Twist binding sites (CACATG). When cocreate two Twist binding sites (CACATG). When combined with the two nucleotid substitutions that prodmbined with the two nucleotid substitutions that produce high-affinity Dorsal binding sites,the modified enuce high-affinity Dorsal binding sites,the modified enhancer now directs a broad pattern of gene expression hancer now directs a broad pattern of gene expression in both the mesoderm and neurogenic ectoderm.in both the mesoderm and neurogenic ectoderm.

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

3-5 The misexpression of Ubx change3-5 The misexpression of Ubx changes the morphology of the fruit flys the morphology of the fruit fly

New patterns of gene expression are produced bNew patterns of gene expression are produced by changing the Ubx expression pattern, the ency changing the Ubx expression pattern, the encoded regulatory protein, or its target enhancers.oded regulatory protein, or its target enhancers.

Antp is one of the genes that it regulates: Ubx reAntp is one of the genes that it regulates: Ubx represses Antp expression in the metathorax of presses Antp expression in the metathorax of developing embryos.developing embryos.

The expression of Ubx in the different tissues of The expression of Ubx in the different tissues of the metathorax depends on regulatory sequencthe metathorax depends on regulatory sequences that encompass more than 80 kb of genomic es that encompass more than 80 kb of genomic DNA.DNA.

The consequences of misexpressing a pattern detThe consequences of misexpressing a pattern determining gene can cause a dramatic change in ermining gene can cause a dramatic change in morphology results.morphology results.

3-6 Changes in Ubx function modify 3-6 Changes in Ubx function modify the morphology of fruit fly embryosthe morphology of fruit fly embryos

Ubx protein can function as a transcriptional reprUbx protein can function as a transcriptional repressor.essor.

The Ubx protein contains specific peptide sequeThe Ubx protein contains specific peptide sequences that recruit repression complexes.nces that recruit repression complexes.

Ubx can be converted into an activator by fusing Ubx can be converted into an activator by fusing the Ubx DNA-binding domain to the potent acthe Ubx DNA-binding domain to the potent activation domain from the viral VP-16 protein.tivation domain from the viral VP-16 protein.

The protein sequences that mediate transcriptionThe protein sequences that mediate transcriptional repression map outside the Ubx homeodomaal repression map outside the Ubx homeodomain and are not present in the Ubx-VP16 fusion in and are not present in the Ubx-VP16 fusion protein .protein .

The misexpression of the Ubx-VP16 fusion proteThe misexpression of the Ubx-VP16 fusion protein causes all of the segments to develop as mesin causes all of the segments to develop as mesothoracic segments.othoracic segments.

The Ubx-VP16 fusion protein produces the same The Ubx-VP16 fusion protein produces the same phenotype as that obtained with Antp.phenotype as that obtained with Antp.

3-7 Changes in Ubx target enhancers 3-7 Changes in Ubx target enhancers can alter patterns of gene expressioncan alter patterns of gene expression

The Ubx protein contains a homeodomain that mThe Ubx protein contains a homeodomain that mediates sequence-specific DNA binding, and ediates sequence-specific DNA binding, and

it also contains a tetrapeptide motif (YPWM) thit also contains a tetrapeptide motif (YPWM) that mediates interactions with Exd.at mediates interactions with Exd.

Ubx binds DNA as a Ubx-Exd dimer.Ubx binds DNA as a Ubx-Exd dimer.

Exd binds to a half-site with the core sequence, TGAT, Exd binds to a half-site with the core sequence, TGAT, Hox proteins such as Ybx bind an adjacent half-site wHox proteins such as Ybx bind an adjacent half-site with a diferent core consensus sequence, A-T-T/G-A/G.ith a diferent core consensus sequence, A-T-T/G-A/G.

This obserbation raises the possibility that target enhancThis obserbation raises the possibility that target enhancers regulated by one Hox protein can rapidly evolve iers regulated by one Hox protein can rapidly evolve into a target enhancer for a different Hox protein.nto a target enhancer for a different Hox protein.

So ,the altering the function or expression of the UbxproSo ,the altering the function or expression of the Ubxprotein or its target enhancers profoundly changes pattertein or its target enhancers profoundly changes patterning in the Drosophila embryos and adults.ning in the Drosophila embryos and adults.

Topic 4 Morphological changes in Topic 4 Morphological changes in crustaceans and insectscrustaceans and insects

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

4-1 Arthropods are remarkably 4-1 Arthropods are remarkably diversediverse

Arthropods embrace five groups: trilobites, hexaArthropods embrace five groups: trilobites, hexapods, crustaceans, myriapods, and chelicerates.pods, crustaceans, myriapods, and chelicerates.

The success of the arthropods derives from their The success of the arthropods derives from their modular architecture.modular architecture.

These organisms are composed of a series of repThese organisms are composed of a series of repeating body segments that can be modified in seating body segments that can be modified in seemingly limitless ways.eemingly limitless ways.

4-2 changes in Ubx expression explai4-2 changes in Ubx expression explain modifications in limbs among the cn modifications in limbs among the c

rustaceansrustaceans

There are two different groups crustaceans, branThere are two different groups crustaceans, branchiopod and isopod. chiopod and isopod.

In branchiopods Scr expression is restricter to heIn branchiopods Scr expression is restricter to head regions where it helps promote the debelopad regions where it helps promote the debelopment of feeding appendages,while Ubx is exprment of feeding appendages,while Ubx is expressed in the thorax where it controls the develoessed in the thorax where it controls the development of swinning limbs.pment of swinning limbs.

In isopods, Scr expression is detected in both the In isopods, Scr expression is detected in both the head and the first thoracic segment(T1), and as head and the first thoracic segment(T1), and as a result, the swimming limb in T1 is transforma result, the swimming limb in T1 is transformed into a feeding appendage.ed into a feeding appendage.

This posterior expansion of Scr was made possibThis posterior expansion of Scr was made possible by the loss of Ubx expression in T1 since Ule by the loss of Ubx expression in T1 since Ubx normally represses Scr expression.bx normally represses Scr expression.

During the divergence of branchiopods and isopDuring the divergence of branchiopods and isopods, the Ubx regulatory sequence changed in iods, the Ubx regulatory sequence changed in isopods. As a result of this change, Ubx expresssopods. As a result of this change, Ubx expression was eliminated in the first thoracicion was eliminated in the first thoracic

segments, and restricted to segments T2-T8. segments, and restricted to segments T2-T8. In Artemia, these head genes are kept off in all 1In Artemia, these head genes are kept off in all 1

1thoracic segments, but in isopods the head ge1thoracic segments, but in isopods the head genes can be expressed in the T1 segment due to nes can be expressed in the T1 segment due to the loss of the Ubx repressor.the loss of the Ubx repressor.

Expression of the Scr gene is restricted to head rExpression of the Scr gene is restricted to head regions of branchiopods, but is expressed in T1egions of branchiopods, but is expressed in T1of isopods. The expression of Scr in T1 causes of isopods. The expression of Scr in T1 causes maxillipeds to develop in place of normal swimaxillipeds to develop in place of normal swimming limbs.mming limbs.

4-3 Why insects lack abdominal 4-3 Why insects lack abdominal limbs?limbs?

The loss of abdominal limbs in insects is due to functionThe loss of abdominal limbs in insects is due to functional changes in the Ubx regulatory protein.al changes in the Ubx regulatory protein.

In insects, Ubx and abd-A repress the expression of a criIn insects, Ubx and abd-A repress the expression of a critical gene that is required for the development of limbtical gene that is required for the development of limbs, call Dll.s, call Dll.

Although Ubx is expressed in metathorax, it does not intAlthough Ubx is expressed in metathorax, it does not interfere with the expression of Dll in that segment, becaerfere with the expression of Dll in that segment, because Ubx is not expressed in the developing T3 legs unuse Ubx is not expressed in the developing T3 legs until after the time when Dll is activated, as a result, Ubtil after the time when Dll is activated, as a result, Ubx does not interfere with limb development in T3.x does not interfere with limb development in T3.

The misexpression of Ubx throughout all of the tThe misexpression of Ubx throughout all of the tissues of the presumptive thorax in transgenic issues of the presumptive thorax in transgenic Drosophila embryos suppresses limb developDrosophila embryos suppresses limb development due to the repression of Dll.ment due to the repression of Dll.

The misexpression of the crustacean Ubx protein The misexpression of the crustacean Ubx protein in transgenic flies does not interfere with Dll gin transgenic flies does not interfere with Dll gene expression and the formation of thoracic liene expression and the formation of thoracic limbs.mbs.

4-4 modification of flight limbs 4-4 modification of flight limbs might arise from the evolution of might arise from the evolution of

regulatory DNA sequencesregulatory DNA sequences

Changes in the Ubx expression pattern appear to Changes in the Ubx expression pattern appear to be responsible for the transformation of swimbe responsible for the transformation of swimming limbs into maxillipeds in crustaceans.ming limbs into maxillipeds in crustaceans.

Ubx in crustaceans, the C-terminal antirepressioUbx in crustaceans, the C-terminal antirepression peptide blocks the activity of the N-terminal n peptide blocks the activity of the N-terminal repression domain.repression domain.

Ubxin insects ,the C-terminal antirepression peptUbxin insects ,the C-terminal antirepression peptide was lost throught mutation.ide was lost throught mutation.

Two possibilities:Two possibilities:

First, the Ubx protein is functionally distinct in flFirst, the Ubx protein is functionally distinct in flies and butterfiles.ies and butterfiles.

Second, each of the approximately five to ten tarSecond, each of the approximately five to ten target genes that are repressed by Ubx in Drosopget genes that are repressed by Ubx in Drosophila have evolved changes in their regulatory hila have evolved changes in their regulatory DNAs so that they are no longer repredded by DNAs so that they are no longer repredded by Ubx in butterflies.Ubx in butterflies.

The Ubx repressor is expressed in the halters of The Ubx repressor is expressed in the halters of dipterans and hindwings of lepidopterans.dipterans and hindwings of lepidopterans.

Different target fenes contain Ubx repressor sites Different target fenes contain Ubx repressor sites in dipterans. These habe been lost in lepidopterin dipterans. These habe been lost in lepidopterans.ans.

An implication of the preceding arguments is thaAn implication of the preceding arguments is that evolutionary changes regulatory DNAs.t evolutionary changes regulatory DNAs.

Topic 5 Genome evolution and Topic 5 Genome evolution and human originshuman origins

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

5-1 Humans contain surprisingly few 5-1 Humans contain surprisingly few genesgenes

The human genome contains only 25000-30000 The human genome contains only 25000-30000 protein coding genes. Before the human genoprotein coding genes. Before the human genome was sequenced, there were popular estimatme was sequenced, there were popular estimates for 100000 protein coding genes.es for 100000 protein coding genes.

Organismal complexity is not correlated with geOrganismal complexity is not correlated with gene number, but instead depends on the number ne number, but instead depends on the number of gene expression patterns.of gene expression patterns.

5-2 The human genome is very 5-2 The human genome is very similar to that of the mouse and similar to that of the mouse and virtually identical to the chimpvirtually identical to the chimp

Mice and humans contain roughly the same Mice and humans contain roughly the same number of genes, approximately 80% of these number of genes, approximately 80% of these genes possess a clear and unique one-to-one genes possess a clear and unique one-to-one sequence alignment with one another between sequence alignment with one another between the two species.the two species.

Most of the remaining 20% of the genes in mice Most of the remaining 20% of the genes in mice and humans differ by virtue of lineage-specific and humans differ by virtue of lineage-specific gene duplication events.gene duplication events.

The chimp and human genomes are even more The chimp and human genomes are even more highly conserved, they vary by an average of highly conserved, they vary by an average of just 2% sequence divergence.just 2% sequence divergence.

The regulatory DNA evolve more rapidly than The regulatory DNA evolve more rapidly than proteins.proteins.

5-3 the evolutionary origins of 5-3 the evolutionary origins of human speechhuman speech

Speech depends on the precise coordination of Speech depends on the precise coordination of the small muscles in our larynx and mouth.the small muscles in our larynx and mouth.

Reduced levels of a regulatory protein called Reduced levels of a regulatory protein called FOXP2 cause severe defects in speech.FOXP2 cause severe defects in speech.

Changes in the expression pattern or changes in Changes in the expression pattern or changes in FOXP2 target genes might be responsible for FOXP2 target genes might be responsible for the ability of FOXP2 to promote speech in the ability of FOXP2 to promote speech in humans.humans.

5-4 How FOXP2 fosters speech in 5-4 How FOXP2 fosters speech in humanshumans

Changes in the FOXP2 expression pattern, changes in itChanges in the FOXP2 expression pattern, changes in its amino acid sequence, and changes in FOXP2 target s amino acid sequence, and changes in FOXP2 target fenes might explain its emergence as an important mefenes might explain its emergence as an important mediator of human speech.diator of human speech.

Some might encode neurotransmitters or other critical siSome might encode neurotransmitters or other critical signals that are expressed within the developing larynx.gnals that are expressed within the developing larynx.

FOXP2 is just one example of a regulatory fene that undFOXP2 is just one example of a regulatory fene that underlies human speech.erlies human speech.

A scenario for the evolution of speech in humans.A scenario for the evolution of speech in humans.

A hypothetical regulatory protein is expressed in A hypothetical regulatory protein is expressed in the neocortex of both chimps and humans.the neocortex of both chimps and humans.

The human gene is strongly expressed at the critiThe human gene is strongly expressed at the critical time in the development of the speech centcal time in the development of the speech center and activates all three hypothetical target geer and activates all three hypothetical target genes in the neocortex, these target gene might enes in the neocortex, these target gene might encode neurotransmitters important for the formncode neurotransmitters important for the formation of the speech center.ation of the speech center.

5-5 The future of comparative 5-5 The future of comparative genome analysisgenome analysis

There is a glaring limitation in our ability to infer There is a glaring limitation in our ability to infer the function of regulatory DNA from simple the function of regulatory DNA from simple sequence inspection .sequence inspection .

In the future it might also be possible to identify In the future it might also be possible to identify changes in the expression profiles of changes in the expression profiles of homologous genes.homologous genes.

Summary Summary

The same concept of differential gene expression can The same concept of differential gene expression can explain the evolution of animal diversity.explain the evolution of animal diversity.

Changes in gene expression during evolution depend on Changes in gene expression during evolution depend on altering the activities of a special class of regulatory altering the activities of a special class of regulatory genes, called pattern determining genes.genes, called pattern determining genes.

There are three major strategies for altering the There are three major strategies for altering the activities of pattern determining genes.activities of pattern determining genes.

We are fast entering a golden era of comparative We are fast entering a golden era of comparative genome analysis.genome analysis.

The EndThe End

Thank you!Thank you!