Download BIOL 404: Molecular Evolution

BIOL 404: Molecular Evolution
Ring of Life
Organelle Genomes
Bacteria
Dr. Erica Bree Rosenblum
Extrachromosomal DNA
Chromosomal
DNA
Extrachromosomal
Elements
Eukaryotes
Archea
Origin of eukaryotes involved
internalization of a eubacterium
Organelle DNA
Most but not all organelle DNA are single
circular genomes (like prokaryotes) but not all
(some linear, some multiple molecules)
Mitochondria - very streamlined, generally no
introns or mobile elements
Chloroplasts (plastids) - lots of noncoding DNA
Many more changes to the “universal genetic
code” in mitochondrial DNA than nuclear DNA
Mitochondria
Origin of mitochondria
Mitochondria are bacterial in origin common ancestor of eukaryotes contained
a mitochondrion-like organelle
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Origin of mitochondrial DNA
Adaptive hypotheses for role of ancient
mitochondrial precursor:
Energy provisioning (aerobic): modern
mitochondria produce ATP used by the cell
Origin of mitochondrial DNA
There is also the possibility that ancient
acquisition of mitochondrial precursor
was non adaptive - it is difficult to test
these alternatives
Oxygen scavenging (aerobic): arose (~2BYA)
when oxygen levels were rising - could have
removed of extra (toxic) oxygen from cells
Hydrogen acquisition (anaerobic): may have
produced hydrogen in an anaerobic environment
Photosynthate acquisition (anaerobic): may
have been photosynthetic and subsequently lost
this trait once in an aerobic environment
Mitochondrial genome architecture
Animals have the smallest mitochondrial genomes
• generally 14-20 kb
• 13 protein coding genes
• 22 tRNA genes
• 2 ribosomal genes
• generally lack introns
• >90% coding
Plants have the largest mitochondrial genomes
• generally 180-1600 kb
• 29-59 protein coding genes
• full set of transfer and ribosomal RNA genes
• have some introns
• >90% noncoding
Mutation in mitochondria
In animals the average substitution rate at
silent sites in mtDNA is 10 - 20 times higher
than in the nuclear genome
This is NOT true in land plants, where the
substitution rates in mtDNA are much lower
than they are in the nuclear genome
Mutation in mitochondria
Mitochondrial DNA exhibits a higher mutation
rate than nuclear DNA in animals
Mitochondria are sites of aerobic respiration and
generate high levels of free oxygen radicals,
producing an internally mutagenic environment
MtDNA frequently replicates within nondividing
cells increasing opportunities for replication
errors per cell cycle
Mitochondria contain multiple genomic copies
increasing mutational targets
Muller’s ratchet
mtDNA (particularly in animals) has increased
mutation rate and reduced ability to shed
mutations by recombination, it is susceptible to
degradation by a process called…
Muller’s ratchet (or mutational meltdown): the
irreversible accumulation of deleterious
mutations
Mutation accumulation is a one way street in non
recombining genomes. Parents cannot make
offspring with fewer deleterious mutations
(except in rare case of back/compensatory mutations)
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Muller’s ratchet
Although Muller’s ratchet is theoretically a
problem, on time scales relevant to species
existence deleterious mutation accumulation in
the mitochondria may not be a big problem
Organelle transmission
In animals mitochondria are uniparentally
inherited with almost no recombination
(rare instances of “paternal leakage”)
In plants mitochondria are uniparentally
inherited with little recombination
In fungi mitochondria are often biparentally
inherited and recombination does occur
Organelle transmission
Organelle transmission
Organelle genomes are replicated ameiotically
So there are bottlenecks in mtDNA
population at every generation
They are generally inherited uniparentally
(usually maternally)
Up to 100,000 organelles per oocyte, but number
organelle genome copies actually passed to
offspring appears to be much smaller than this
(anywhere from ~2 in covs to ~ 300 in flies)
Thus genetic drift plays large role in
mtDNA evolution
Effective population sizes of organelle
genomes are thus relative small
(also because of uniparental inheritance)
Organelle effective population size
Organelle effective population size
People usually assume organelle genomes have
effective pop sizes about 1/4 of nuclear genes
(in diploids each reproduction involves 4 nuclear
gene copies but only one organelle gene copy)
In actuality, empirical evidence suggests
that effective population sizes of
mitochondrial genes compared to nuclear
genes is quite variable across taxa and
doesn’t always follow this 1:4 “rule”
But this doesn’t take into account:
- differences in selective interference
in nuclear and organelle genomes
- variance in reproductive success
among sexes (eg: if fewer male breeders)
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Mitochondrial-nuclear cooperation
There is rampant “cooperation” between
mitochondrial and nuclear genomes.
In yeast ~850 nuclear encoded proteins
are imported to the mitochondria (~2000
for invertebrates and ~4000 for vertebrates)
Many of these genes were probably
transferred early in evolution from
mitochondrial DNA to nucleus
Mitochondrial-nuclear cooperation
Nuclear genes with mitochondrial
functions make proteins “tagged” with N
terminal sequence that guides them to the
mitochondrial membrane
Proteins binds to membrane receptors
and are threaded through pores
Some could also be nuclear in origin but
have acquired new organelle associated
functions
Mitochondrial-nuclear cooperation
If there is a higher mutation rate in the
mitochondria, why are any genes retained
there?
Mitochondrial-nuclear coadaptation
How to study mitochondrial-nuclear
cooperation/conflict/coadaptation?
One hypothesis is that organelle genomes
tend to produce hydrophobic proteins
that get integrated into the organelle
membrane which are difficult to import
Rand et al 2004
Origin of chloroplasts
Origin of chloroplasts
Second colonization event in eukaryotes:
Cyanobacterium into the ancestor of green
plants and red algae gave rise to the plastid
(chloroplast in photosynthetic tissues)
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Origin of chloroplasts
Organelle specific patterns of evolution
Plastids are similar to mitochondria in
that there has been a lot of organellenuclear gene sharing.
Overall organelle DNA is likely to have
different evolutionary dynamics than
nuclear counterpart due to differences in:
Unlike mitochondria (which are vertically
inherited), plastids have been horizontally
transferred across several lineages
Mutation rate: generally higher than
nucDNA in animals and lower in plants
Effective population size: uniparental
inheritance may lead to lower Ne and
stronger effects of drift
Selection: similar to sex chromosomes
uniparental inheritance can create sexspecific patterns of selection.
Nuclear-organelle coordination of gene expression
Because each cell can contain multiple
organelles, and each organelle can contain
multiple copies of its genome, there can be
up to a 5,000 fold disparity between copy
number of nuclear and organellar genomes!
Nuclear-organelle coordination of gene expression
Thus, gene expression must be coordinated
Woodson and Chory 2008
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