Organelle Evolution

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Organelle Evolution

• Genome size and composition

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Plastid
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mitochondrion
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Plant chloroplasts
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Plant cp genomes
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• Mesostigma
• Marchantia

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Beige genes absent in Marchantia
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Land plant chloroplast genome

• 120,000 bp
• 23S, 16S, 4.5S, and 5S rRNA
• 37 genes encoding tRNA
• 4 genes encoding subunits RNA polymerase
• the large subunit of RUBISCO
• 9 components of photosystems I and II
• 6 genes encoding parts of ATP synthase
• genes for 19 of the 60 ribosomal proteins

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Chloroplast Gene Transfer

• NUPTS
• Arabidopsis has 11kb from 17 insertions
• rice chromosome 10 has a 33kb and a 131kb
  insertion and 26 more over 80bp each

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Chloroplast Gene Transfer

• NUPTS
• Arabidopsis has 11kb from 17 insertions
• rice chromosome 10 has a 33kb and a 131kb
  insertion and 26 more over 80bp each
• rate estimates from tobacco chloroplasts
• 1 transfer in 5 million leaf cells
• 1 transfer in 16 000 pollen grains

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Plant mitochondria
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Plant mitochondria
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Leishmania sp.
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Mitochondrial Gene Transfer

• NUMTS
• complete mt genome sequences in cat nuclei
• gt296 in humans, from 106 to 14,654bp each
• rice chromosome 10 has 57 NUMTS ranging from
  80-2552bp

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Mitochondrial Gene Transfer

• NUMTS
• complete mt genome sequences in cat nuclei
• gt296 in humans, from 106 to 14,654bp each
• rice chromosome 10 has 57 NUMTS ranging from
  80-2552bp
• rate estimates
• 1 transfer in 20,000 yeast cells

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Mechanisms

• mitochondria of plants and yeast can fuse and
  divide
• tobacco pollen cells break down chloroplasts
  during maturation
• yeast cells use bits of mt DNA to repair double
  stand breaks in the nucleus

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Protein Targeting
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RNA polymerase

• Mitochondria don't encode their own RNA
  polymerase
• Not bacterial type of RNA polymerase
• Probably phage-derived
• Some species have multiple nuclear encoded RNA
  polymerases

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RNA editing

• C?U substitution
• Mainly in highly constrained sites
• 1st and 2nd codon positions (not 3rd)
• Changes in phobicity
• Genes under selective constraints
• Can affect future gene transfers to the nucleus

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Maternal vs. Paternal transmission

• Most plants inherit cytoplasm exclusively
  maternally, as far as we know
• Some inherit paternally
• Mitochondria in Cucurbita melo, C. Sativus, Musa
  acuminita, Sequoia sempervirens, Mytilidae
  (Mussels)?
• Chloroplast in some Passiflora, Pinus,
• Occasional mixed inheritance of mitochondria in
  some animals, plants --gt recombination?
• Can't tell in Cryptosporidium no DNA in
  mitochondria!

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Rearrangements

• Chloroplast and mitochondrial genomes
• Important characters for phylogenetics
• Common in many groups
• May be adaptive (Cui et al 2006)?
• Genes clustered according to function
• Neighboring genes co-transcribed
• Clusterings unlikely by chance (compared to
  inferred ancestral arrangement)?

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Repeated, recent, and diverse transfers of a
mitochondrial gene to the nucleus in flowering
plants

• Adams, Daley, Qiu, Whelan Palmer

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Procedure

• extract total DNA from 277 angiosperms
• Southern blot using universal rps10 probe
• low substitution rate in plant mt genomes
• high copy number in plant mt genomes
• 26 losses among 277 plants

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• loss from mt
• intron loss in mt
• exon but not intron loss from mt (?)?

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Procedure

• plot inferred losses on a phylogenetic tree to
  see what pattern emerges
• - inclusive count is 26 independent losses
• - one bullet means checked by PCR
• - two bullets means investigated further

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Procedure

• amplify some putatively nucleus-encoded rps10
  genes to check - all showed
• - higher nucleotide substitution rates
• - lack of RNA editing sites
• - loss of group II introns
• investigate a few in further detail fuchsia,
  carrot, spinach, maize, oxalis, lettuce,
  passionflower
• conduct import experiments
• phylogenetic analysis of rps10

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Fuchsia

• got its targeting sequence from HSP70
• sequence homology
• two shared introns
• precedent seen in rps11 in rice

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Carrot

• inserted into hsp22 and stole targeting info

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Carrot

• inserted into hsp22 and stole targeting info
• presequence is cleaved upon import

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Spinach, Maize, Oxalis

• no targeting sequences
• imported to a protease-insensitive location in
  membrane potential-dependent manner
• like rice

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Lettuce

• inserted into a non-targeted metalloprotease

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Lettuce

• inserted into a non-targeted metalloprotease
• also has no targeting sequence, but is still
  imported to soy and potato mitochondria without
  cleavage

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Summary

• fuchsia, carrot, and lettuce rps10 have all
  inserted into different nuclear genes
• spinach, maize, and oxalis rps10s all lack
  targeting sequences, but are distantly related
• arabidopsis rps10 has a targeting sequence but
  seems not to have inserted into a gene
• therefore at least 7 independent transfers

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Phylogenetic Analysis

• long branch nuclear rps10 sequences go together

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Phylogenetic Analysis

• long branch nuclear rps10 sequences go together
• individually they branch with their
  mitochondria-encoded relatives

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KH tests
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KH tests
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Conclusions

• at least 7 and likely 26 independent transfers in
  the sampled angiosperms
• sampled angiosperms are only 2 of angiosperm
  diversity, so this could be the tip of the
  iceberg
• Only 1 gene sampled, out of the entire
  mitochondrial genome

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