7/31/2019 Mitochondrial Genome Evolution

1/14

Mitochondrial Genome

EvolutionLevel 3 Molecular Evolution and

Bioinformatics

Jim Provan

7/31/2019 Mitochondrial Genome Evolution

2/14

References

Gray MW, Burger G, Lang BF (1999) MitochondrialevolutionScience283: 1476-1481

Leblanc C, Richard O, Kloareg B et al. (1997) Origin and

evolution of mitochondria: what have we learnt fromred algae?Current Genetics31: 193-207

Lang BF, Gray MW, Burger G (1999) Mitochondrialgenome evolution and the origin of eukaryotesAnnual Review of Genetics33: 351-397

Turmel M, Otis C, Lemieux C (2003) The mitochondrialgenome ofChara vulgaris: insights into themitochondrial DNA of the last common ancestor ofgreen algae and land plantsPlant Cell15: 1888-1903

7/31/2019 Mitochondrial Genome Evolution

3/14

7/31/2019 Mitochondrial Genome Evolution

4/14

The animal mitochondrial genome

Daphnia pulex(15,333bp)

14kb - 42kb in size

Generally same 37 genes:12S and 16S rRNA

13 proteins22 tRNAs

No recombination

Little intergenic DNA

No intronsVariable control region

Own genetic code

7/31/2019 Mitochondrial Genome Evolution

5/14

The plant mitochondrial genome

~200kb - 2400kb in size

Extra genes:Open Reading Frames

Ribosomal proteins

Chloroplast tRNAs

Generally multi-circular

Over 90% non-coding DNA

Universal genetic codeMarchantia polymorpha(184,000 bp)

7/31/2019 Mitochondrial Genome Evolution

6/14

Diversity of mitochondrial genomes

SizeNon-coding DNA

Mutation rate High

Very Low14kb - 42kb

Recombination

Introns

Universal genetic code

Low

Variable17kb - 180kb

/

Mostly

Very Low

Very High184kb - 2,400kb

Animals Fungi Plants

7/31/2019 Mitochondrial Genome Evolution

7/14

Reclinomonas americana- theancestral mitochondrial genome?

Total of 97 genes:All protein-coding genesfound in all mtDNAs

18 protein genes unique toReclinomonas

Four genes (rpoA-D)encode a eubacteria-likeRNA polymerase (2)

Vestigial prokaryoticoperon organisation

Universal genetic code

7/31/2019 Mitochondrial Genome Evolution

8/14

7/31/2019 Mitochondrial Genome Evolution

9/14

Mitochondrial phylogeny - a separateorigin for plant mtDNA?

Presence of unique 5S RNAgene in plant mtDNA andstructural difference led to

theory of separate origin ofmitochondria for plants

Analysis of mitochondrialproteins gave topologysimilar to nuclear gene-

derived phylogenies acquired before radiation ofeukaryotes

Neurospora crassa

Podospora anserina

Aspergillus nidulans

Saccharomyces cerevisiae

Homo sapiens

Mus musculusXenopus laevis

Strongylocentrosus purpuratus

Drosophila yakuba

Oryza sativaTriticum aestivum

Oenothera berteriana

Marchantia polymorpha

Prothoteca wickerhamiiChondrus crispus

Cyanidium caldariumAcanthamoeba castellanii

cox1/cox2/cobamino acid sequence

7/31/2019 Mitochondrial Genome Evolution

10/14

Mitochondrial phylogeny - a separateorigin for plant mtDNA?

rpl2 rps19 rpl22 rps3 rpl16 rpl29 rps17

Nucleus

Escherichia coliRickettsia prowazekii

rpl2 rps19 rps3 rpl16

Mitochondrion

Marchantia polymorphaNephroselmis olivacea

Acanthamoeba castellaniiDictyostelium discoideum

Naegleria gruberiReclinomonas americana

Jakoba libera

7/31/2019 Mitochondrial Genome Evolution

11/14

Diversity of streptophytemitochondrial genomes

Taxon

NephroselmisMesostigma

ChaetosphaeridiumChara

MarchantiaArabidopsisBetaOryza

Size (bp)

45,22342,424

56,57467,737

186,609366,924368,799490,520

% coding

78.586.6

76.390.7

65.036.833.0

?

Genes

6365

6768

69494853

Gp I

44

914

7000

Gp II

03

213

25232023

Introns

7/31/2019 Mitochondrial Genome Evolution

12/14

Diversity of streptophytemitochondrial genomes

Radical changes in size, % coding DNA, gene contentand intron content between Chara/Marchantiaandangiosperms

Despite differences in size, CharamtDNA is verysimilar to MarchantiamtDNA:

All except 9 of 68 conserved genes lie within blocks ofcolinear sequences

% AT-content (59.1) closer to land plants (55.2-57.6) thanto other green algae (65.6-67.8)

Group I introns

7/31/2019 Mitochondrial Genome Evolution

13/14

Acquisition of mitochondria

Species in yellow lackmitochondria

Entamoeba histolyticahasobviously lost mitochondria

Suggests mitochondriawere gained at position B

Other evidence suggestsposition A:

Hydrogenosomes ofTrichomonassimilar tomitochondria

Presence of chaperonins

Anemonia sulcataArtemia salina

Saccharomyces cerevisiaeMucor racemosus

Volvox carteriiOxytricha nova

Prorocentrum nicansOchromonas danicaAchlya bisexualis

Dictyostelium discoideumEntamoeba histolyticaNaegleria gruberi

Physarium polycephalumEuglena gracilis

Crithidia fasciculataTrypanosoma brucei

Hexamita inflata

Giardia lambliaTrichomonas foetus

Vairimorpha nectarixHalobacterium volcanii

Thermoplasma acidophilumSulfolobus solfataricus

Escherichia coliRickettsia rickettsiiMycoplasma gallisepticum

Small subunitrRNA tree

B

A

7/31/2019 Mitochondrial Genome Evolution

14/14

Final remarks

Mitochondria seem to be monophyletic in origin,derived from a common protomitochondrial ancestor

Continuing quest for mtDNAs older thanReclinomonas americanacontaining more genes

Studies of early-diverging protists to find minimally-diverged -proteobacterial relatives of mitochondria

Implications for phylogeny of eukaryotes

Evolution of plant mitochondrial genomes radicallydifferent