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Organelle genomes

Organelle genomes. Small but essential genomes Multiple organelles per cell; multiple genomes per organelle (20 – 20,000 genomes per cell, depending on cell type) Organized in nucleo -protein complexes called nucleoids

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Organelle genomes

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  1. Organellegenomes Small but essential genomes Multiple organelles per cell; multiple genomes per organelle (20 – 20,000 genomes per cell, depending on cell type) Organized in nucleo-protein complexes called nucleoids Non-Mendelian inheritance; usually but not always maternally inherited Encode necessary but insufficient information to elaborate a fully functional organelle Many nuclear gene products required for organelle function Considerable cross-talk between nuclear and organelle genetic systems

  2. Thefate of endosymbioticgenomes Reduced coding content of organelle genomes  Functional gene transfer to nucleus with protein targeted back to organelle Evolution of mitochondrial genome coding content Evolution of plastid genome coding content

  3. Plastid genome coding content • Chloroplast Genome Database: http://chloroplast.cbio.psu.edu/ • Generally conserved among land plants, more variable among algae • Genes for plastid gene expression • rRNAs, tRNAs • ribosomal proteins • RNA polymerase • Genes involved in photosynthesis • 28 thylakoid proteins • Photosystem I (psa) • Photosystem II (psb) • ATP synthase subunits (atp) • NADH dehydrogenase subunits (nad) • Cytochrome b6f subunits (pet) • RUBISCO large subunit (rbcL) • (rbcS is nuclear encoded)

  4. Group II introns, which are widely believed to be the progenitors of the nuclear splicing machinery (the spliceosome) and its substrates, comprise a large ribozyme (catalytic RNA) and the coding sequence of a reverse transcriptase. Group II introns are found in mitochondrial, chloroplast and bacterial genomes and a majority of them behave as retrotransposons.

  5. The mitochondrial genome

  6. Human genome = nuclear genome + mitochondrial genome Mitochondrial genome 16569 bp 37 genes HUMAN NUCLEAR GENOME 24 chromosomes (haploid) 3200 Mbp 30,000 genes

  7. 1-10 m small Mitochondria are present in the cytoplasm of all eukaryote cells of animals and higher plants and also in some microorganisms (algae, fungi, protozoa).

  8. Mitochondrial Genome • Small circular genome • >1000 copies/ cell • 16569 bp 44% G+C • H- Strand Guanines • L- Strand Cytosines • D- Loop 7S DNA

  9. Mitochondrion plays a role in: • Energy production Oxidative phosphorilation (OXPHOS) • Maintaining the intracellular homeostasis • Protecting the rest of the cell from reactive oxygen species (ROS) • Apoptosis  important development and disease

  10. Mitochondria-the point of no return-to live or to die Pro-caspase 3 Smac/ Diablo XIAP ATP Caspase 3 casp9 AIF Bcl2 Apaf1 AIF substrates Apoptosis Nuclear apoptosis

  11. Genome Structure • The mitochondrial genome is a circle, 16.6 kb of DNA. A typical bacterial genome is 2-4 Mbp. • The two strands are notably different in base composition, leading to one strand being “heavy” (the H strand) and the other light (the L strand). • Both strands encode genes, although more are on the H strand. • A short region (1121 bp), the D loop (D = “displacement”), is a DNA triple helix: there are 2 overlapping copies of the H strand there. • The D loop is also the site where most of replication and transcription is controlled. • Genes are tightly packed, with almost no non-coding DNA outside of the D loop. In one case, two genes overlap: they share 43 bp, using different reading frames. Human mitochondrial genes contain no introns, although introns are found in the mitochondria of other groups (plants, for instance).

  12. The Human Mitochondrial Genome 2 - 10 copies/mitochondrion • Circular • ~ 16 kb (some plants ~100 kb!) • Crowded (~40 genes) • 13 genes involved in oxidative phosphorylation + other genes (DNA pol, rDNAs, tRNAs) • Most proteins in mitochondria are imported from cytoplasm • 100,000 copies of mitochondrial DNA in ovum

  13. Organization of the human genome Limited autonomy of mt genomes mt encodednuclear NADH dehydrog 7 subunits >41 subunits Succinate CoQ red 0 subunits 4 subunits Cytochrome b-c1 comp 1 subunit 10 subunits Cytochrome C oxidase 3 subunits 10 subunits ATP synthase complex 2 subunits 14 subunits tRNA components 22 tRNAs none rRNA components 2 components none Ribosomal proteins none ~80 Other mt proteins none mtDNA pol, RNA pol etc.

  14. The Human Mitochondrial Genomeexpression unlike nucleus genome… • Transcription controlled by nuclear proteins: 3 promoters- * H1: H-strand; complete transcription of one strand of mtDNA * L: L-strand; complete transcription of light strand of mtDNA * H2: Synthesis of 2 rRNAs • Transcripts then procesed into individual genes prior to translation

  15. Coding- Non-coding 37 genes 28 genes H- strand 9 genes L- strand 24 genes specify a mature RNA product 2 mitochondrial rRNA molecules (23S and 16S) 22 tRNA molecules 13 genes specify polypeptides

  16. H strand enriched in G L strand enriched in C

  17. Mitochondrial Genetic code is somewhat different… HumanMito Standard AGA Ter Arg AGG Ter Arg AUA, AUU Met Ile UGA Trp Ter UGA encodes trp at low efficiency in E. coli Plastid genetic code: GUG, UUG, AUU, CUG can initiate translation

  18. Mitochondrial inheritance pattern - uniparentalmaternal in animals Paternal inheritance in gymnosperms, some angiosperms

  19. Endosymbiont Hypothesis • endosymbiont hypothesis: originally proposed in 1883 by Andreas Schimper, but extended by Lynn Margulis in the 1980s. • Mitochondrial ribosomal RNA genes and other genes show that the original organism was in the alpha-proteobacterial family (similar to nitrogen-fixing bacteria) • Evidence: • mitochondria have their own DNA (circular) • the inner membrane is more similar to prokaryotic membranes than to eukaryotic. By the hypothesis, the inner membrane was the original prokaryotic membrane and the outer membrane was from the primitive eukaryote that swallowed it. • mitochondria make their own ribosomes, which are of the prokaryotic 70S type, not the eukaryotic 80S type. • mitochondria are sensitive to many bacterial inhibitors that don’t affect the rest of the eukaryotic cell, such as streptomycin, chloramphenicol, rifampicin. • mitochondrial protein synthesis starts with N-formyl methionine, as in the bacteria but unlike eukaryotes. • Most of the original bacterial genes have migrated into the nucleus. • Eukaryotes that lack mitochondria generally have some mitochondrial genes in their nucleus, evidence that their ancestors had mitochondria that were lost during evolution.

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