Chapter 19Chapter 19Comparative GenomiComparative Genomics and the Evolution cs and the Evolution of Animal Diversityof Animal Diversity

周亚萍 生科 1 班

200331060105

The evolution of diversity among organisms is not due to the presence of different specialized genes. Rather,animal evolution depends on deploying the same set of genes in different ways.

Most animal phyla fall into three major groups:the lophotrochozoans,ecdysozoans,and deuterostomes.

The figure shows the relationships among those animals whose genomes have been sequenced to date

Where did the evolutionary diversity come from?

How do genes acquire new patterns of expression during evolution?

O U T L I N E• Most Animals Have Essentially the

Same Genes• Three Ways Gene Expression is

Changed during Evolution• Experimental Manipulations that

Alter Animal Morphology• Morphology Changes in Crustaceans

and Insects• Genome Evolution and Human

Origins

Topic 1 Most Animal Have EssTopic 1 Most Animal Have Essentially The Same Genesentially The Same Genes

Comparison of the currently available Comparison of the currently available genomes reveals one particularly striking genomes reveals one particularly striking feature:different animals share essentially feature:different animals share essentially the same genes. the same genes.

98%98% conservation in the protein coding gconservation in the protein coding genes between human and chimp.enes between human and chimp.

The conservation between human and mThe conservation between human and mouse is overouse is over 80%80%..

Phylogenetic tree showing gene duplication of the fibroblast Phylogenetic tree showing gene duplication of the fibroblast growth factor genes(FGF)growth factor genes(FGF)

1-2 How Does Gene 1-2 How Does Gene Duplication Give Rise to Duplication Give Rise to

Biological DiversityBiological Diversity The increase in gene number seen in The increase in gene number seen in

vertebrates is largely due to gene vertebrates is largely due to gene duplication.But how lead to increased duplication.But how lead to increased morphological diversity?morphological diversity?

There are two models for how duplication There are two models for how duplication genes can create diversity:genes can create diversity:

FirstFirst,the duplication process creates genes ,the duplication process creates genes encoding related proteins with slightly encoding related proteins with slightly different activities.different activities.

SecondSecond,duplication genes acquire new ,duplication genes acquire new regulatory DNA sequences.regulatory DNA sequences.

Topic 2 Three Ways Gene Topic 2 Three Ways Gene Expression is Changed Expression is Changed EvolutionEvolution

Changes in gene expression during evolution depend on altering the activities of a special class of regulatory genes,called pattern determining genes. How changes in the deployment or activities of these pattern determining genes produce diversity during evolution?

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

• Changes in their Changes in their expressionexpression profiles. profiles.

• Changes in the Changes in the functionfunction of the encoded of the encoded regulatory proteins .regulatory proteins .

• Changes in the Changes in the enhancersenhancers that are that are regulatory and regulated by pattern regulatory and regulated by pattern determining proteins.determining proteins.

Fig:Summary of the three strategies for altering the roles of pattern determining genes.

Topic 3 Experimental Topic 3 Experimental Manipulations that alter Manipulations that alter Animal MorphologyAnimal Morphology

How the morphology of the fruit How the morphology of the fruit fly can be altered by manipulation fly can be altered by manipulation the activities of specific pattern the activities of specific pattern determining genes?determining genes?

Then apply these strategies to Then apply these strategies to the interpretation of the the interpretation of the evolutionary diversification seen evolutionary diversification seen in different groups of arthropods.in different groups of arthropods.

3-1 Changes in Pax6 Expression 3-1 Changes in Pax6 Expression Create Ectopic EyesCreate Ectopic Eyes

The most notorious pattern The most notorious pattern determining gene is determining gene is Pax6Pax6,which ,which controls controls eyeeye developmentdevelopment in most or in most or all animals.all animals.

Changes in the expression pattern Changes in the expression pattern of the of the Pax6Pax6 gene are probably gene are probably responsible for some of the responsible for some of the morphological diversity seen among morphological diversity seen among the eyes of different animals.the eyes of different animals.

Pax6Pax6 is normally expressed within devel is normally expressed within developing eyes.oping eyes.

But when misexpressed in the wrong tisBut when misexpressed in the wrong tissues,sues,Pax6 Pax6 causes the development of causes the development of extextra eyesra eyes in those tissues. in those tissues.

Figure shows Misexpression of Pax6 and eye formation in DrosophiFigure shows Misexpression of Pax6 and eye formation in Drosophila.la.

(a) Wild-type fly (b) Abnormal leg with misplaced eye.The eye and (a) Wild-type fly (b) Abnormal leg with misplaced eye.The eye and legs arise from imaginal disks in the larvae.legs arise from imaginal disks in the larvae.

Adult eye

3-2 Changes in Antp Expression Tr3-2 Changes in Antp Expression Transform Antennae into Legsansform Antennae into Legs

A second Drosophila pattern determining gene, A second Drosophila pattern determining gene, AntpAntp(An(Antennapedia),controls the development of the middle segmetennapedia),controls the development of the middle segment of the thorax,the nt of the thorax,the mesothoraxmesothorax,which produces a pair of le,which produces a pair of legs that are morphologically distant from the forelegs and higs that are morphologically distant from the forelegs and hindlegs.ndlegs.

AntpAntp encodes a homeodomain regulatory protein that is n encodes a homeodomain regulatory protein that is normally expressed in the mesothorax of developing embryo.ormally expressed in the mesothorax of developing embryo.

The gene is not expressed,for example,in the developing hThe gene is not expressed,for example,in the developing head tissues.But a dominant ead tissues.But a dominant AntpAntp mutation,caused by a chro mutation,caused by a chromosome inversion, brings the mosome inversion, brings the AntpAntp protein coding sequenc protein coding sequence under the control of a “foreign” regulatory DNA that mee under the control of a “foreign” regulatory DNA that mediates gene expressing in head tissues,including the antenndiates gene expressing in head tissues,including the antennae. ae.

A dominant mutation in the Antp gene results in the homeotic transformation of antennae into legs.

3-3 Importance of Protein Function:3-3 Importance of Protein Function:Interconversion of ƒtz and AntpInterconversion of ƒtz and Antp

Two related pattern determining genes in Drosophila,the Two related pattern determining genes in Drosophila,the segmentation genesegmentation gene ftz(fushi tarazu) and the homeotic gene Antp.

The two encoded proteins are related and contain very siThe two encoded proteins are related and contain very similar DNA-binding domains(homeodomains)milar DNA-binding domains(homeodomains)

AntpAntp contains a tetrapeptide sequence motifcontains a tetrapeptide sequence motif, , YPWMYPWM,,whicwhich mediates interactions with a ubiquitous regulatory proteih mediates interactions with a ubiquitous regulatory protein calledn called ExdExd(Extradenticle)(Extradenticle)

In contrast,In contrast, FtzFtz contains a pentapeptide sequence,contains a pentapeptide sequence,LRALLLRALL,,which mediates interactions with a different ubiquitous regwhich mediates interactions with a different ubiquitous regulatory protein,ulatory protein,FtzF1FtzF1..

Figure:DuplicatioFigure:Duplication of ancestral genn of ancestral gene leading to Antp e leading to Antp and ƒtz.and ƒtz.

3-4 Subtle Changes in an Enhancer Sequence can Produce New Patterns of Gene Expression

The third mechanismThe third mechanism for evolutionary diversity is changes for evolutionary diversity is changes in the target enhancers that are regulated by pattern deterin the target enhancers that are regulated by pattern determining genes.This mechanism is nicely illustrated by the Domining genes.This mechanism is nicely illustrated by the Dorsal regulatory gradient in the early fly embryorsal regulatory gradient in the early fly embryo..

Target enhancers that contain Target enhancers that contain low-affinitylow-affinity Dorsal binding Dorsal binding sites are expressed in the mesoderm,where there are sites are expressed in the mesoderm,where there are high lhigh levelsevels of the Dorsal gradient. of the Dorsal gradient.

Enhancers with Enhancers with high-affinityhigh-affinity sites are expressed in neurog sites are expressed in neurogenic ectoderm,where there are intermediate and enic ectoderm,where there are intermediate and low levelslow levels of the gradient. of the gradient.

Single nucleotide substitutions that covert each sSingle nucleotide substitutions that covert each site into an optimal Dorsal binding site cause the mite into an optimal Dorsal binding site cause the modified enhancer to be activated in a broader patteodified enhancer to be activated in a broader pattern.rn.

When combined with the two nucleotide substituWhen combined with the two nucleotide substitutions that produce high-affinity Dorsal binding site,tions that produce high-affinity Dorsal binding site,the modified enhancer now directs a broad pattern the modified enhancer now directs a broad pattern of gene expression in both the mesoderm and neurof gene expression in both the mesoderm and neurogenic ectoderm.ogenic ectoderm.

A modified enhancer, containing optimal Dorsal sA modified enhancer, containing optimal Dorsal sites,Twist activator sites,and Snail repressor is expites,Twist activator sites,and Snail repressor is expressed only in the negurogenic ectoderm where theressed only in the negurogenic ectoderm where there are low levels of the Dorsal gradientre are low levels of the Dorsal gradient.

Figure:Regulation of transgene expression in the early Drosophila embryo

3-5 The Misexpression of 3-5 The Misexpression of UbxUbx Changes th Changes the Morphology of the Fruit Flye Morphology of the Fruit Fly

The analysis of Drosophila pattern determining The analysis of Drosophila pattern determining gene called gene called UbxUbx illustrates all three principles of e illustrates all three principles of evolutionary change:new patterns of gene expressivolutionary change:new patterns of gene expression are produced by changing the Ubx expression on are produced by changing the Ubx expression pattern,the encoded regulatory protein,or its targpattern,the encoded regulatory protein,or its target enhancers.et enhancers.

UbxUbx encodes a homeodomain regulatory protei encodes a homeodomain regulatory protein that controls the development of the third thorn that controls the development of the third thoracic segment,the acic segment,the metathoraxmetathorax.And it specifically r.And it specifically repress the expression of genes that are acquired fepress the expression of genes that are acquired for the development of or the development of mesothoraxmesothorax..

Ubx mutants cause the transformation of the metathoraUbx mutants cause the transformation of the metathorax into a duplicated mesothorax.x into a duplicated mesothorax.

In adult flies,the mesothorax contains a pair of legs and wiIn adult flies,the mesothorax contains a pair of legs and wings,while the mesothorax contains a pair of legs and halterngs,while the mesothorax contains a pair of legs and halteres.es.

Misexpression of Ubx in the mesothorax results in the loss of wings.

3-6 Changes in Ubx Function Modifty the Morphology3-6 Changes in Ubx Function Modifty the Morphology

The Ubx protein can function as a transcriptional repressor thThe Ubx protein can function as a transcriptional repressor that precludes the expression of Antp and other “mesothorax”at precludes the expression of Antp and other “mesothorax”genes in the developing metathorax.genes in the developing metathorax.It is not currently known how Ubx functions as a repressor.HoIt is not currently known how Ubx functions as a repressor.However,the Ubx protein contains speific peptide sequences thawever,the Ubx protein contains speific peptide sequences that recruit repression complexes. t recruit repression complexes.

Figure:Changing the regulatory activities of the Ubx protein.

3-7 Changes in Ubx Target Enhancers Can Alter Patterns of Gene Expression

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

Many homeotic regulatory proteins interact with Many homeotic regulatory proteins interact with Exd and bind a composite Exd-Hox recognition seqExd and bind a composite Exd-Hox recognition sequence.uence.

Exd binds to a half-site with the core sequence,TExd binds to a half-site with the core sequence,TGAT,whereas Hox proteins such as Ubx bind an adjGAT,whereas Hox proteins such as Ubx bind an adjacent half-site with a different core consensus sequacent half-site with a different core consensus sequence,A-T-T/G-A/G.ence,A-T-T/G-A/G.

InterconversiInterconversion of Labial aon of Labial and Ubx bindinnd Ubx binding sitesg sites

Topic 4 Morphological Changes Topic 4 Morphological Changes In Crustaceans And InsectsIn Crustaceans And Insects

The first two mechanismsThe first two mechanisms,,changes in changes in the expression and function of pattern the expression and function of pattern determining genes,can account for determining genes,can account for changes in limb morphology seen in changes in limb morphology seen in certain crustaceans and insects.certain crustaceans and insects.

The third mechanism,changes in The third mechanism,changes in regulatory sequences,might provide an regulatory sequences,might provide an explanation for the different patterns of explanation for the different patterns of wing development in fruit flies and wing development in fruit flies and butterflies.butterflies.

4-1 Arthropods Are Remarkably divers4-1 Arthropods Are Remarkably diversee

Arthropods embrace five groups:trilobites(sadly extiArthropods embrace five groups:trilobites(sadly extinct),hexapods(such as insects),crustaceans(shrimp,lobnct),hexapods(such as insects),crustaceans(shrimp,lobsters,crabs,and so on),myriapods(centipedes and millisters,crabs,and so on),myriapods(centipedes and millipedes),and chelicerates(horseshoe crabs,spiders,and spedes),and chelicerates(horseshoe crabs,spiders,and scorpions).corpions).

4-2 Changes in Ubx Expression Explain Modifications in Limbs Among the Crustaceans

Artemia belongs to an order of crustaceans known as branchiopodsbranchiopods.

A different order of crustaceans called isopodsisopods.Isopods contain swimming limbs on the second through eighth thoracic segments just like the branchiopods.

The limbs on the first thoracic segment of isopods have been modified.They are smaller than the others and function as feeding limbs,which called maxilmaxillipedslipeds

Changing morphologies in two different groups of crustaceans.

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

Why Insects lack Abdominal Limbs?Why Insects lack Abdominal Limbs?

Evolutionary changes in Ubx protein function

What is the basis for this functional difference between the two Ubx protein?

It turns out that the crustacean protein has a short motif containing 29 amino acid residues that block repression activity.When this sequence is deleted, the crustacean Ubx protein is just as effective as the fly protein at repressing Dll gene expression.

Comparison of Ubx in crustacean and in insects.

4-4 Modification of Flight Limbs Might Arise from the Evolution of Regulatory DNA Sequences

Ubx has dominated morphological change in arthropods.

Approximately five to ten genes are repressed by Ubx.These genes encode proteins that are crucial for the growth and patterning of the wings.

Changes in the regulatory DNA of Ubx target genes

Topic 5 Genome Evolution and Human Origins

Consider Functional diversity among different mammals.

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

5-1 Humans Contain Surprisingly Few Genes

A variety of gene prediction programs are used to identify protein coding genes in whole-genome assemblies. Predicted genes are sometimes confirmed by independent tests-most frequently,the isolation of cDNAs corresponding to the encoded mRNAs.There’re numerous inaccuracies in the intro-exon structure of predicted genes due to the degeneracy and simplicity of the sequence signals required for splicing.

The human genome contains only 25000-30000 protein coding genes.

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

5-2 The Human Genome Is very Similar to that of the Mouse and Virtually Identical to t

he ChimpMice and humans contain roughly the same numMice and humans contain roughly the same number of genes-about 28000 protein coding genes.ber of genes-about 28000 protein coding genes.The chimp and human genomes are even more hiThe chimp and human genomes are even more hightly conserved.ghtly conserved.Regulatory DNA evolve more rapidly than proteinRegulatory DNA evolve more rapidly than proteins.Perhaps the limited sequence divergence betws.Perhaps the limited sequence divergence between chimps and humans is sufficient to alter the een chimps and humans is sufficient to alter the activities of several key regulatory DNAsactivities of several key regulatory DNAs.

5-3 The Evolutionary Origins of Human Speech

Alone humans possess the capacity for precise communication in the form of speech and written language.

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.

The FOXP2 gene was isolated in a variety of mammals,including mice,chimps,and orangutans.

But in humans there’re two amino acid residues at position 303 and 325 that are unique to humans:thr to asn(T to N) at position 303 and asn to ser(N to S) at position 325.Perhaps these changes have altered the function of the human FOXP2 protein.

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

FIG 17 Summary of amino acid changes in the FOXP2 proteins of mice and primates.

FIG 18 Comparison of the FOXP2 gene sequences in human,chimp, and mouse.

5-4 How FOXP2 Fosters Speech in Humans

The three mechanisms for changing the function of regulatory genes such as FOXP2.

• Changes in the FOXP2 expression pattern• Changes in the FOXP2 amino acid

sequence• Changes in FOXP2 target genes Those are might explain the emergence as

an important mediator of human speech.

FIG 19 A scenario for the evolution of speech in humans

5-5 The Future of Comparative Genome Analysis

It’s possible to infer the function of roughly half of all prIt’s possible to infer the function of roughly half of all predicted protein coding genes based solely on primary DNedicted protein coding genes based solely on primary DNA sequence information.A sequence information.If a codon exists,which regulatory DNAs that mediate simIf a codon exists,which regulatory DNAs that mediate similar patterns of gene expression share,then it might be poilar patterns of gene expression share,then it might be possible to infer both the timing and sites of gene expressiossible to infer both the timing and sites of gene expression by simply scanning the DNA sequences associated with n by simply scanning the DNA sequences associated with any given gene.any given gene.The continuing development of new computational methThe continuing development of new computational methods and the availability of new genome assemblies offer ods and the availability of new genome assemblies offer exciting prospects for the use of comparative methods to exciting prospects for the use of comparative methods to reveal the mechanism of evolutionary diversity. reveal the mechanism of evolutionary diversity.

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