Mitochondria

1. Mitochondria Molecular evolution of the mitochondrial genome

2. Mitochondria

3. The powerhouse of eukaryotic cells

4. The powerhouse of eukaryotic cells

5. The powerhouse of eukaryotic cells

6. The powerhouse of eukaryotic cells

7. Anderson et al. 1981 Nature 290, 457 - 465 ABSTRACT “The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located.”

8. Anderson et al. 1981 Nature 290, 457 - 465 ABSTRACT (continue) “The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.”

9. Human mitochondrial genome H-strand (Heavy strand) 16,569 base pairs L-strand (Light strand) Anderson et al. 1981 Nature290, 457 - 465

10. Nucleus or mitochondria Mitochondria Nucleus Burger et al. TRENDS in Genetics Vol.19 No.12 December 2003

11. Conclusion1:Mitochondrial proteins • There are more protein in the mitochondria than those encoded in the mitochondrial genome • The mt proteins that are not encoded in the genome are imported from the nucleus • The mitochondrial genome is different between species

12. Animal mitochondrial genomes The main difference is usually gene order. Control region

13. T P ND6 E CR F cyt b 12S T1 P1 ND61 E1 CR1 T2 P2 ND62 E2 CR2 F cyt b 12S Variation in genes orderBird genome Ancestral gene order (chicken) Hypothetical intermediate stage (albatrosses) xxxxxxxxxxxxxx xxx xxxxx Derived gene order (crow) P ND6 E NC T CR F cyt b 12S

14. Echinodermata

15. Molecular tree Porifera Cnidaria Plathyelminthes Lophotrochozoa Annelids Mollusca Arthropodes Ecdysozoa Nematodes Echinodermata Chordata

16. Variation in genes order

17. Amoebidium (Ichthyosporean) Spizellomyces (Fungi) Tetrahymena (Ciliate) Eukaryotes mitochondrial genome: anything goes !!! Homo (Metazoa) After Burger et al. 2003

18. Mitochondrial genome content Homo (Metazoa) genes Arabidopsis (Viridiplantae) introns non coding

19. Mitochondrial intron • There is no spliceosome in the mitochondria. (a spliceosome is a complex of specialized RNA and protein subunits that removes introns from a transcribed pre-mRNA). • Mitochondrial introns are catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors. • There are two self-spicing intron types: Group I and Group II introns.

20. Secondary structureof type 1intron Tetrahymena thermophilus 26S 26S

23. group III introns are present in eukaryotic nucleus

24. Gene classes and size of mitochondrial genomes After Burger et al. 2003

25. Mitochondrial gene classesIn Eukaryotes After Burger et al. 2003

26. Reclinomonas Genus of small bacterivorous zooflagellates. The single species, R. americana Flavin & Nerad, 1993, is known from freshwater and soil habitats in the United States of America and New Zealand.

27. Conclusion2:Mitochondrial genome • The genome shape and content is different between Eukaryotes lineages • There were independent gene losses in the different Eukaryotes lineages • The genome evolve via duplications, deletions, and inversion, • Gene order can help to reconstruct the evolutionary relationships

28. Origin of the mitochondrial genome: the endosymbiosis theory Multi- cellular Protists Monera

29. 18S rRNA tree [TREE vol. 13, no. 12 December 1998]

30. Microsporidia Microsporidia are anaerobic protists. They are unusual in lacking mitochondria.

31. Trichomonads The trichomonads are an order of anaerobic protists. Most are either parasites or other endosymbionts of animals Trichomonas vaginalis

32. Diplomonads The diplomonads are a group of flagellates protists, most of which are parasitic. Most diplomonads are double cells: they have two nuclei, each with four associated flagella. They lack both mitochondria and Golgi apparatus. Giardia lamblia

33. 18S rRNA tree [TREE vol. 13, no. 12 December 1998]

34. [Sciences vol. 300, no. 5626 pp.1703]

35. A B = C Outgroup Reconstructed tree B A A C = B Outgroup C Outgroup Long Branch Artifact (LBA) True tree A B C Outgroup 100

36. Origin of the mitochondrial genome: the endosymbiosis theory Multi- cellular Protists Monera

37. Conclusion3:Mitochondria and Eukaryotes • Eukaryotes without mitochondria have never exited (Archeozoa) • Eukaryotes without mitochondria have lost their mitochondria (they usually have mitosomes or hydrogenosomes)

38. Origin of mitochondria Mitochondria

39. Ehrlichia ruminantium Ehrlichia canis Anaplasma phagocytophilum Anaplasma marginale Rickettsiales Wolbachia pipientis Neorickettsia sennetsu Rickettsia sibirica Rickettsia akari Rickettsia prowazekii Arabidopsis thaliana Reclinomonas americana Monosiga brevicollis Mitochondria Caenorhabditis elegans Homo sapiens Saccharomyces cerevisiae Neurospora crassa Rhizobium leguminosarum Agrobacterium tumefaciens 50/ 1.0 Sinorhizobium meliloti Alpha-proteobacteria phylogenetic tree based on rpoB,atpD, cox2, cox3, and cob sequences Mesorhizobium loti Rhizobiales 68/1.0 Brucella melitensis Rhodopseudomonas palustris Bradyrhizobium japonicum Silicibacter pomeroyi 56/0.95 67/1.0 Jannaschia sp. CCS1 67/ 1.0 Paracoccus denitrificans Rhodobacterales Rhodobacter sphaeroides 74/1.0 Hyphomonas neptunium 73/ 1.0 Caulobacter crescentus Caulobacterales Zymomonas mobilis Sphingomonadales Novosphingobium aromaticivorans Micavibrio sp. EPB Magnetospirillum magnetotacticum 58/0.77 Rhodospirillales Rhodospirillum rubrum Gluconobacter oxydans Desulfovibrio desulfuricans 69/1.0 Delta- Proteobacteria Geobacter metallireducens Myxococcus xanthus Bdellovibrio bacteriovorus Bacteriovorax marinus 0.1

40. Rickettsiales • The Rickettsiales, are an order of small proteobacteria. Most of them are endosymbionts or parasites of other cells. • Like many obligate, intracellular, microbial pathogens, they have small genomes of (<1.5 Mb) as a result of reductive genome evolution.

41. Conclusion3:Mitochondria and Bacteria • Mitochondria are proteobacteria and probably the sister clade of Rickettsiales. • Mitochondrial genome < 400 kbp • Rickettsiales genomes > 1,000 kbp

42. Genome size comparisons Lang et al. 1999 Annual Review of Genetics vol. 33: 351-397

43. Question • Where Did All the Mitochondrial Genes Go?

44. 1- Gene loss • Gene loss from mtDNA appears to be an irreversible process because there are no indications (introns excepted) of widespread and substantial gene flux between mtDNAs of different species or from other genomes to mtDNA. • Few exceptions….

45. MutS in Coral (Sarcophyton) [J Mol Evol (1998) 46:419–431]

46. MutS in Coral (Sarcophyton) Nuclear encoded DNA which is involved in mt DNA repair NJ tree using Dayhoff distance [J Mol Evol (1998) 46:419–431]

47. Other genes that migrate to the mitochondrial genome • Chloroplast-like tRNA genes in angiosperm (flowering plant) mtDNA. • Plasmid-derived DNA and RNA polymerase genes in fungal, plant, and several protist mtDNAs. • Mitochondrial introns. • ALL OTHER GENES WERE DERIVED VERTICALLY from the proto-mitochondrial ancestor

48. Gene loss • Genes whose function became obsolete in the setting of a specialized organelle, such as those involved in nucleotide, lipid, and amino acid biosynthesis, must have been eliminated from most mtDNAs early on in evolutionary history.

49. Question • Where Did All the Mitochondrial Genes Go?

50. 2- Take-over of the corresponding function by nuclear genes • For example, in the ciliate protozoans Tetrahymena pyriformis or the cnidaria, the mtDNA encodes, respectively, only seven and two distinct tRNA genes. • To ensure translation of all codons in mitochondrial protein-coding genes, missing mitochondrial tRNAs are imported from the cytosol (proven only in the ciliate).