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…

09_01_Germ_somatic1.jpg

09_02_Germ_somatic2.jpg

09_03_altered.genes_part1.jpg

Genetic Change Mutation

09_03_altered.genes_part2.jpg

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

09_05_Gene.duplicate.jpg

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…

09_06_globin.1.jpg

Gene duplication / deletion

09_07_globin.2.jpg

Duplication Divergence

• New gene copy is free to mutate

• Not all duplications lead to functional new genes (pseudogenes)

• Impact of gene deletions?

09_09_exon.jpg

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

09_11_exon.arrange.jpg

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

09_13_conjugation.jpg

Horizontal Transfer: organisms exchanging genes

Conjugation animation

09_14_promiscuous.jpg

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

09_15_Phylogen.trees.jpg

Evolutionary descent

09_16_Ancestral.gene.jpg

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

09_17_Human_chimp.jpg

Conserved synteny

Rediers et. al., Microbiology 2004

Sample genome analysis

PST v PSB

0

1000

2000

3000

4000

5000

6000

0 1000 2000 3000 4000 5000 6000

PST position

PS

B p

os

itio

n

Series1

Synteny in Pseudomonas

PST v PP

0

1000

2000

3000

4000

5000

6000

0 1000 2000 3000 4000 5000 6000

PST position

PP

po

sit

ion

Series1

PST v PA

0

1000

2000

3000

4000

5000

6000

0 1000 2000 3000 4000 5000 6000

PST position

PA

po

sit

ion

Series1

09_19_human_mouse1.jpg

“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?

09_21_Fugu.introns.jpg

Introns (noncoding DNA) are non-essential

09_22_genetic.info.jpg

Conserved sequences: comparing distant genomes

Small subunit of rRNA