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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