Generating Diversity: how genes and genomes evolve

Erin “They call me Dr. Worm” Friedman29 September 2005

Intro/Background

• Why do we care about generating diversity?• What exactly is mutation?• How does evolution act on mutations?• How does evolution work on a molecular

scale?• It’s not just about frog mating calls…

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Genetic Change Mutation

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Point Mutations• Nucleotide change, addition, deletion

• Silent Mutation – same AA (synonymous)• Sense Mutation – different AA (nonsynonymous)• Nonsense Mutation – stop codon (translation termination)

Plotkin et. al., Nature 2004

Generating Point Mutations

• Replication Errors (Polymerase isn’t perfect)– Human rate 1 in 1010

• Chemical mutagens or radiation• Repair failure after such DNA damage

Sickle Cell Anemia

• Caused by a point mutation in beta chain of hemoglobin (GAGGTG)

• Changes glutamic acid to valine– What kind of mutation is this?

• Autosomal Recessive Disorder• Cell morphology

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html

Sickle Cell Evolution

• Sickle cell anemia vs. sickle cell trait (het)

• Low oxygen Acidity sickling

• Link between sickle cell trait and malaria

• Positive selection for sickle cell trait in some regions with high malaria incidence

http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html

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Gene duplication / deletion

Globin Gene Evolution

• Especially important in larger, multicellular organisms– Diffusion doesn’t cut it

• Multiple duplication events• Primitive animals have one globin chain;

higher vertebrates have two• Beta-globin duplicated / mutated again

(fetal, adult) and each product duplicated…

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Gene duplication / deletion

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Duplication Divergence

• New gene copy is free to mutate• Not all duplications lead to functional new

genes (pseudogenes)• Impact of gene deletions?

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Exon Duplication

Fig. 9-10

Exon Shuffling• Recombination between non-

homologous genes• A few thousand exons could

explain protein variability today

• Combinations of different exon elements

• (symbols = different protein domains)

Exon shuffling

• Can bacteria use exon duplication / shuffling to form a functional gene?

• Why would big introns be beneficial for generating diversity in this manner?

Transposable Elements

• Parasitic DNA sequences

• Can disrupt function, alter regulation, or make new genes by bringing along gene segments with it

• Inverted repeats• Transposase binding

domains

http://engels.genetics.wisc.edu/Pelements/fig1.html

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Transposons

Transposable Elements in regulatory regions

Common human example of gene inactivation from transposon insertion: Factor VIII hemophilia

Transposons as a tool

• Transposable elements can be used to study particular genes

• Knock out genes and look for a phenotype (reverse genetics)

• Drosophila P-Element (transposon)– Can carry different genes, map insertion by

phenotype

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Horizontal Transfer: organisms exchanging genes

Conjugation animation

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Consequences of Horizontal Transfer

• Gene duplication• Rapid evolution• Bacterial antibiotic resistance

– Some strains of TB are resistant to 9 antibiotics– “Drug resistance may have contributed to the 58

percent rise in infectious disease deaths among Americans between 1980 and 1992.” (Mayo Clinic)

– Where in genome would resistance genes live?

What Now?

• We can use this information to reconstruct an evolutionary tree

Analyzing Genomes• Homologous genes have common ancestry,

similar nt sequences– Finding homologues with BLAST

• Different genome segments evolve differently– Highly conserved / essential genes = constrained

• Purifying selection removes dysfunctional individuals

• Positive selection preserves beneficial mutations• Genetic Drift: random, unconstrained mutation• How we measure mutation rate

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Evolutionary descent

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Why reconstruct ancestor sequences?

• Can be used to study evolution rates– Why can’t you just compare 2 genes? – Measuring rates with dN/dS, PAML

• Evolution rate is a good screen for looking for candidate genes (compare gene to ancestor, not to homologous gene):– Some genes likely evolve rapidly (e.g. those involved

in infection, defense)– Highly conserved, essential genes likely evolve slowly

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Conserved synteny

Rediers et. al., Microbiology 2004

Sample genome analysis

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“Junk” DNA

Exons more highly conserved than introns: different evolutionary constraints in different parts of genome

What kind of selection is acting on the exons?

What phenomenon is taking place in the intron?

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Introns (noncoding DNA) are non-essential

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Conserved sequences: comparing distant genomes

Small subunit of rRNA