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Mitochondria Molecular evolution of the mitochondrial genome.

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Presentation on theme: "Mitochondria Molecular evolution of the mitochondrial genome."— Presentation transcript:

1 Mitochondria Molecular evolution of the mitochondrial genome

2 Mitochondria

3 The powerhouse of eukaryotic cells Krebs Cycle Glycolysis 364Yield ATP

4 The powerhouse of eukaryotic cells

5

6

7 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.” Anderson et al Nature 290,

8 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.” Anderson et al Nature 290,

9 Human mitochondrial genome Anderson et al Nature 290, ,569 base pairs H-strand (Heavy strand) L-strand (Light strand)

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

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 Control region The main difference is usually gene order.

13 The human mtDNAs contain only 13 polypeptide genes, all of which encode essential components of OXPHOS (Oxidative Phosphorylation). MtDNA encodes the 12S and 16S rRNA genes and the 22 tRNA genes required for mitochondrial protein synthesis. The remaining mitochondrial OXPHOS proteins, the metabolic enzymes, the DNA and RNA polymerases, the ribosomal proteins and the mtDNA regulatory factors are all encoded by nuclear genes, synthesized in the cytosol and then imported into the organelle (Shoffner & Wallace 1995, Wallace et al. 1997a). Human mitochondrial genome

14 Variation in genes order Bird genome Derived gene order (crow) cyt b CR 12S ND6TPEF cyt b CR 12S ND6NC TF PE Ancestral gene order (chicken) Hypothetical intermediate stage (albatrosses) cyt b CR 1 12S ND6 1 T1T1 P1P1 E1E1 FCR 2 ND6 2 T2T2 P2P2 E2E2 xxxxxxxxxxxxxxxxxxxxxx

15 Echinodermata

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

17 Variation in genes order

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

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

20 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.

21 Secondary structure of type 1 intron 26S Tetrahymena thermophilus

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24 group III introns are present in eukaryotic nucleus

25 After Burger et al Gene classes and size of mitochondrial genomes

26 After Burger et al Mitochondrial gene classes In Eukaryotes

27 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.

28 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

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

30 18S rRNA tree [TREE vol. 13, no. 12 December 1998]

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

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

33 Diplomonads Giardia lamblia 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.

34 18S rRNA tree [TREE vol. 13, no. 12 December 1998]

35 [Sciences vol. 300, no pp.1703]

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

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

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

39 Origin of mitochondria Mitochondria

40 0.1 Ehrlichia ruminantium Ehrlichia canis Anaplasma phagocytophilum Anaplasma marginale Wolbachia pipientis Neorickettsia sennetsu Rickettsia sibirica Rickettsia akari Rickettsia prowazekii Arabidopsis thaliana Reclinomonas americana Monosiga brevicollis Caenorhabditis elegans Homo sapiens Saccharomyces cerevisiae Neurospora crassa Rhizobium leguminosarum Agrobacterium tumefaciens Sinorhizobium meliloti Mesorhizobium loti Brucella melitensis 68/1.0 Rhodopseudomonas palustris Bradyrhizobium japonicum Silicibacter pomeroyi Jannaschia sp. CCS1 67/1.0 Paracoccus denitrificans Rhodobacter sphaeroides Hyphomonas neptunium Caulobacter crescentus 74/1.0 56/0.95 Zymomonas mobilis Novosphingobium aromaticivorans 50/ 1.0 Micavibrio sp. EPB 67/ 1.0 Magnetospirillum magnetotacticum Rhodospirillum rubrum 58/ / 1.0 Gluconobacter oxydans Desulfovibrio desulfuricans Geobacter metallireducens 69/1.0 Myxococcus xanthus Bdellovibrio bacteriovorus Bacteriovorax marinus Delta- Proteobacteria Mitochondria Rickettsiales Rhodospirillales Sphingomonadales Rhodobacterales Rhizobiales Caulobacterales Alpha-proteobacteria phylogenetic tree based on rpoB, atpD, cox2, cox3, and cob sequences

41 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.

42 Rickettsiales Some are notable pathogens, including Rickettsia, which causes a variety of diseases in humans Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts.

43 Rickettsiales Wolbachia is one of the most abundant bacterial endosymbionts, associated with up to 76% of all arthropods and most of the filarial nematodes. No pathogenic species are known. The bacterium is transovarially inherited from female to offspring. In the arthropods, it manipulates the host's reproduction system to ensure an effective transmission to the next generation. There are four sex-ratio distortion systems induced by Wolbachia; feminization, male killing, parthenogenesis induction and cytoplasmic incompatibility (CI).

44 Cytoplasmic incompatibility (CI) It results in more or less frequent abortive embryonic development. CI occurs when infected males mate with either uninfected females or with females infected by incompatible Wolbachia strains, which leads to the propagation of Wolbachia-infected individuals in a population.

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

46 Lang et al Annual Review of Genetics vol. 33: Genome size comparisons

47 Question Where Did All the Mitochondrial Genes Go?

48 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….

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

50 The MMR machinery removes base substitution and frameshift mismatches that escape from DNA polymerase proofreading activity after DNA replication, increasing DNA replication fidelity 100- to fold. In E. coli, the factors that are exclusively involved in MMR are encoded by mutS, mutL, and mutH genes (Lahue et al., 1989). Mismatch repair (MMR) in bacteria

51 MMR in eukaryotes

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

53 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

54 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.

55 Question Where Did All the Mitochondrial Genes Go?

56 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).

57 Many tRNA in animal mitochondrial genomes

58 Few tRNA in coral mt genomes Metridium After Beagley et al. 1998

59 Question Where Did All the Mitochondrial Genes Go?

60 rnl rns GV F cox2 A nad5 nad2 A L2L2 I1I1 nad1 S2S2 C 271 cox1 Y2Y2 364 nad4L nad3 D nad6 E H nad4 P S1S1 atp9 T Y1Y1 247 I2I2 atp8 K atp6 R2R2 R1R1 cox3 cob N L1L1 Q W 3- Mt genes migrated to the nucleus ATP synthase subunit 9

61 Burger et al. TRENDS in Genetics Vol.19 No.12 December 2003 Nucleus Nucleus or Mitochondria Mitochondria Complex 5 ATP synthase

62 The ATP synthase is a large protein complex with a proton channel that allows re-entry of protons.

63 ATP subunit 9 story In human and other animals ATP 9 is encoded in the nuclear genome. In most fungi, plants, and protists ATP 9 is encoded in the mitochondrial genome.

64 Metazoa phylogenetic tree Coral Bilateria Sponges Fungi Nuclear ATP9 Mitochondrial ATP9

65 There is no ATP9 gene !!

66 Amphimedon How to explain the evolution of ATP9 in animal ??? Negombata Tethya Axinella Geodia Oscarella Iphiteon Sympagella Coral Bilateria Fungi Sponges

67 How to explain the evolution of ATP9 in animal ??? There was independent transfer of ATP 9 to the nuclear genome.

68 Cox 2 in plants For example, in leguminous plants, the active gene coding for cytochrome oxidase subunit 2 (cox2) is nuclear in some species, whereas in other taxa (as in all other plants), cox2 is mtDNA-encoded. In soybean, an inactive mitochondrial gene copy has been detected in addition to an active nuclear one, whereas this gene has been completely eliminated from the mtDNA of cowpea, a close relative.

69 Conclusions We can find that some mt genes migrate to the nuclear genome, when some species have the gene in their mitochondrial genome while other have the same genes encoded in their nuclear genome. What about mt genes that migrated to the nuclear genome in the ancestor of eukaryotes?????

70 HSP 70 Gupta and Singh Current Biology (1994) 4: The 70 kilodalton heat shock proteins are a family of ubiquitously expressed proteins. Proteins with similar structure exist in virtually all living organisms. The Hsp70s are an important part of the cell's machinery for protein folding, and help to protect cells from stress.

71 HSP 70 Human_cyt Yeast_cyt Maize_cyt Giardia_cyt Human_er Yeast_er Giardia_er Pea_chl Synechosystis Drosophila_mt Yeast_mt E.coli Other_Bacteria Many_Bacteria Archae Bacteria Plant Animal Cytoplasm Endoplasmic reticulum Chloroplast Mitochondria

72 Conclusions Some genes that are encoded in the nucleus and expressed in the mitochondria are remnant of the ancestral mitochondrial genome. What about eukaryotes without mitochondria?

73 ValRS tree Hashimoto, Tetsuo et al. (1998) PNAS 95,

74 Aminoacyl-tRNA synthetase Aminoacyl-tRNA synthetases covalently link an amino acid to a a tRNA, that contains the triplet anti-codon for that amino acid

75 ValRS indel Hashimoto, Tetsuo et al. (1998) PNAS 95, amino-acid gap TV= Trichomonas GL=Gardia

76 Remark about INDEL and phylogeny INDEL=insertion deletion (also called GAP) MPGGGASAASGRLLTAAEQRGSREAAGSASRSGFGGSGGGRGGASGPG MPGGGASAASGRLLTAAE ASRSGFGGSGGGRGGASGPG MPGGGASAASGRLLTAAEQRGSREAAGSASRSGFGGSGGGRGGASGPG MPGGGASAASGRLLTAAE ASRSGFGGSGGGRGGASGPG A B C D E outgroup Indel: rare changes as phylogenetic markers

77 Indels to solve phylogeny Gupta et al (2005) showed that it is possible to use indels and protein signatures to solve phylogeny of bacteria.

78 ValRS indel Hashimoto, Tetsuo et al. (1998) PNAS 95, amino-acid gap TV= Trichomonas GL=Gardia

79 cpn60 tree Roger, Andrew J. et al. (1998) Proc. Natl. Acad. Sci. USA 95, Rickettsiales Nuclear encoded

80 Conclusions We can find that some genes of mitochondrial origin in the genome of amitochondriate eukaryotes which indicate that they once had mitochondria.


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