Transcript Mitochondrial Genome Evolution

Mitochondrial Genome
Evolution
Level 3 Molecular Evolution and
Bioinformatics
Jim Provan
References
Gray MW, Burger G, Lang BF (1999) “Mitochondrial
evolution” Science 283: 1476-1481
Leblanc C, Richard O, Kloareg B et al. (1997) “Origin and
evolution of mitochondria: what have we learnt from
red algae?” Current Genetics 31: 193-207
Lang BF, Gray MW, Burger G (1999) “Mitochondrial
genome evolution and the origin of eukaryotes”
Annual Review of Genetics 33: 351-397
Turmel M, Otis C, Lemieux C (2003) “The mitochondrial
genome of Chara vulgaris: insights into the
mitochondrial DNA of the last common ancestor of
green algae and land plants” Plant Cell 15: 1888-1903
The mitochondrion
Primary site of oxidative
phosphorylation
Contains own genome
Gene sequences suggest
closest relationship with
-proteobacteria
Believed to be of
endosymbiotic origin
The animal mitochondrial genome
14kb - 42kb in size
Generally same 37 genes:
12S and 16S rRNA
13 proteins
22 tRNAs
Daphnia pulex
(15,333bp)
No recombination
Little intergenic DNA
No introns
Variable control region
Own genetic code
The plant mitochondrial genome
~200kb - 2400kb in size
Extra genes:
Open Reading Frames
Ribosomal proteins
Chloroplast tRNAs
Marchantia polymorpha
(184,000 bp)
Generally multi-circular
Over 90% non-coding DNA
Universal genetic code
Diversity of mitochondrial genomes
Animals
Fungi
Plants
14kb - 42kb
17kb - 180kb
184kb - 2,400kb
Very Low
Variable
Very High
High
Low
Very Low
Recombination

/

Introns



Universal genetic code

Mostly

Size
Non-coding DNA
Mutation rate
Reclinomonas americana - the
ancestral mitochondrial genome?
Total of 97 genes:
All protein-coding genes
found in all mtDNAs
18 protein genes unique to
Reclinomonas
Four genes (rpoA-D)
encode a eubacteria-like
RNA polymerase (2’)
Vestigial prokaryotic
operon organisation
Universal genetic code
Ancestral and derived mitochondrial
genomes
Ancestral
Many genes
Bacteria-like rRNA genes
Complete set of tRNAs
Mostly coding sequence
Gene clusters
Standard genetic code
Derived
Loss of genes
Divergent rDNA / rRNA
High mutation rate
Non-coding DNA
Biased codon usage
Non-standard genetic
code
Mitochondrial phylogeny - a separate
origin for plant mtDNA?
Neurospora crassa
Podospora anserina
Aspergillus nidulans
Saccharomyces cerevisiae
Homo sapiens
Mus musculus
Xenopus laevis
Strongylocentrosus purpuratus
Drosophila yakuba
Oryza sativa
Triticum aestivum
Oenothera berteriana
Marchantia polymorpha
Prothoteca wickerhamii
Chondrus crispus
Cyanidium caldarium
Acanthamoeba castellanii
cox1/cox2/cob amino acid sequence
Presence of unique 5S RNA
gene in plant mtDNA and
structural difference led to
theory of separate origin of
mitochondria for plants
Analysis of mitochondrial
proteins gave topology
similar to nuclear genederived phylogenies 
acquired before radiation of
eukaryotes
Mitochondrial phylogeny - a separate
origin for plant mtDNA?
rpl2
rps19
rpl22
rps3
rpl16
rpl29
rps17
rpl2
rps19
rps3
rpl16
Nucleus
Mitochondrion
Escherichia coli
Rickettsia prowazekii
Marchantia polymorpha
Nephroselmis olivacea
Acanthamoeba castellanii
Dictyostelium discoideum
Naegleria gruberi
Reclinomonas americana
Jakoba libera
Diversity of streptophyte
mitochondrial genomes
Introns
Taxon
Size (bp) % coding
Genes
Gp I Gp II
Nephroselmis
Mesostigma
45,223
42,424
78.5
86.6
63
65
4
4
0
3
Chaetosphaeridium
Chara
56,574
67,737
76.3
90.7
67
68
9
14
2
13
Marchantia
Arabidopsis
Beta
Oryza
186,609
366,924
368,799
490,520
65.0
36.8
33.0
?
69
49
48
53
7
0
0
0
25
23
20
23
Diversity of streptophyte
mitochondrial genomes
Radical changes in size, % coding DNA, gene content
and intron content between Chara/Marchantia and
angiosperms
Despite differences in size, Chara mtDNA is very
similar to Marchantia mtDNA:
All except 9 of 68 conserved genes lie within blocks of
colinear sequences
% AT-content (59.1) closer to land plants (55.2-57.6) than to
other green algae (65.6-67.8)
Group I introns
Acquisition of mitochondria
Anemonia sulcata
Small subunit
Artemia salina
rRNA tree
Saccharomyces cerevisiae
Mucor racemosus
Volvox carterii
Oxytricha nova
Prorocentrum nicans
Ochromonas danica
Achlya bisexualis
Dictyostelium discoideum
Entamoeba histolytica
Naegleria gruberi
B
Physarium polycephalum
Euglena gracilis
Crithidia fasciculata
Trypanosoma brucei
Hexamita
inflata
A
Giardia lamblia
Trichomonas foetus
Vairimorpha nectarix
Halobacterium volcanii
Thermoplasma acidophilum
Sulfolobus solfataricus
Escherichia coli
Rickettsia rickettsii
Mycoplasma gallisepticum
Species in yellow lack
mitochondria
Entamoeba histolytica has
obviously lost mitochondria
Suggests mitochondria
were gained at position B
Other evidence suggests
position A:
Hydrogenosomes of
Trichomonas similar to
mitochondria
Presence of chaperonins
Final remarks
Mitochondria seem to be monophyletic in origin,
derived from a common protomitochondrial ancestor
Continuing quest for mtDNAs older than
Reclinomonas americana containing more genes
Studies of early-diverging protists to find minimallydiverged -proteobacterial relatives of mitochondria
Implications for phylogeny of eukaryotes
Evolution of plant mitochondrial genomes radically
different