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RECONSTRUCTING A “UNIVERSAL TREE”

University of Illinois. RECONSTRUCTING A “UNIVERSAL TREE”. All living things share same common ancestor. Classical view. Prokaryotes. Eukaryotes. 1977: C. Woese. 3 “primordial kingdoms” (or domains). Carl Woese (1928-2012)

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RECONSTRUCTING A “UNIVERSAL TREE”

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  1. University of Illinois RECONSTRUCTING A “UNIVERSAL TREE” All living things share same common ancestor Classical view Prokaryotes Eukaryotes 1977: C. Woese 3 “primordial kingdoms” (or domains) Carl Woese (1928-2012) “… famous for defining the Archaea (a new domain or kingdom of life)” Archaea Eucarya Bacteria - based on ribosomal RNA sequence comparisons Aside: Archaea are not just extremophiles “...the large numbers of environmental rRNA gene sequences...show that [archaea] are present in almost all environments examined...” Robertson Curr Opin Microbiol 2006

  2. 1989: Iwabe - rooting the universal tree - if set of duplicated genes is present in all 3 lineages, then duplication must have occurred in their common ancestor Fig. 5.40 • can use one gene (eg. Gene A2) as an outgroup when comparing • the other one (Gene A1) in all 3 lineages

  3. - Translational elongation factorsEF-G and EF-Tu are homologous and both genes are present in all life forms … so ancient duplication prior to divergence of 3 superkingdoms Fig. 5.41 Bacterial lineage diverged prior to archaeal & eukaryotic ones

  4. Plant-animal-fungal trichotomy Eucarya Bacteria Archaea Fig. 5.39 Where would you place the root on this tree?

  5. Maximum parsimony analysis of a – tubulin sequences “Bootstrap values above 50% are indicated above the nodes … and decay values (additional steps needed to collapse a node) below.” “…all parsimony and distance-based analyses of four large and diverse data sets support a sister-group relationship between animals and fungi.” Baldauf & Palmer PNAS 90:11558, 1993

  6. “Six hypothesized supergroups of eukaryotes” Lane & Archibald Trends Ecol Ecol 23:268, 2008

  7. ENDOSYMBIOTIC ORIGIN OF ORGANELLES 1910 - Mereschkowsky – morphological similarities between chloroplasts/mitochondria and bacteria 1960’s - DNA and ribosomes discovered in chloroplasts/mitochondria 1970 - Margulis – physiological, biochemical similarities… late 1970’s - Gray, Doolittle (Halifax) - first molecular evidence for endosymbiotic origin, from ribosomal RNA data eg. chloroplast & cyanobacterial sequences are more similar than either is to nuclear homologue….

  8. Fig. 5.45

  9. Dot = divergence point of a-proteobacterial and mitochondrial lineages chloroplast How do you interpret the data in this figure? Phylogenetic tree based on SSU ribosomal RNA data mitochondrial Gray PNAS 86: 2267, 1989

  10. Protists are very diverse unicellular eukaryotes Tree based on ribosomal RNA data Fig. 5.39 And certain of them (a few? lineages) lack mitochondria

  11. Did such protist lineages diverge before time of mitochondrial endosymbiotic event? … or did they lose their mitochondria later on? 1997- 98 Mitochondrial-type genes for heat shock proteins, etc … found in nucleus of Microsporidia, Giardia… 1999 - additional sequence data places Microsporidia within fungal clade 2003– Giardia actually has remnant mitochondria mitosome Nature 426: 172, 2003

  12. Brown Nat Rev Genet 4:121, 2003

  13. What features of this figure are out of date? Evolutionary pathway for origin of eukaryotic cell Many genes transferred to nucleus … a few retained in organelle & others lost Alberts Fig. 14-56

  14. Chimeric nature of eukaryotic nuclear genomes Eukaryotic genomes have bacterial-type and archaeal-type genes Fig. 5.43 Certain genes for DNA replication/repair, transcription/translation… shared by archaea & eukaryotes (but absent in bacteria) Possible explanations: 1. Eukaryotic ancestor - archaeal, but bacterial-type genes acquired through horizontal transfer - from organelles (bacterial endosymbiotic origin) - more recent direct transfer from bacteria 2. Eukaryotic ancestor - chimeric fusion of bacterial & archaeal-type genomes

  15. Model for origin of nucleus-cytosol compartmentalization “in the wake of mitochondrial origin” Martin & Koonin Nature 44:41, 2006

  16. HORIZONTAL GENE TRANSFER (p. 359-366) - lateral transfer of genetic information from one genome to another (eg. between two species) Mechanisms: • Transformation • - via free DNA (vector not essential) 2. Transduction - via bacteriophage or virus 3. Conjugation in bacteria - via conjugative plasmid Estimated that ~ 10-18% of E.coli genome due to LGT eg. lactose operon (milk sugar lactose used as carbon source in mammalian colon)

  17. Detecting lateral gene transfer 1. Odd distribution patterns or unexpectedly high similarity to homologues in distant species 2. Unusual nucleotide composition (eg. codon usage bias, GC content) 3. Incongruent phylogenetic trees B A C A B C True tree Inferred tree Fig. 7.22

  18. Implications of lateral gene transfer? 1. Acquisition of new function 2. Replacement of “native” gene with “captured” one 3. In bacteria, acquired genes for particular function may be co-ordinately regulated (operon) 4. Acquisition may re-define ecological niche of microbe

  19. “Web-of-life” Doolittle “Uprooting the tree of life” Sci.Amer. 282:90, 2000 www.whoi.edu/cms/images/oceanus/2005/4/v43n2-teske_edwards1en_8591.gif Was early cellular life communal? How rampant was (is) lateral gene transfer - especially among microbes? “Highways of gene sharing” among prokaryotes? Transposable elements carry along “foreign genes?” and Doolittle Science 284: 2124, 1999

  20. Informational genes: machinery for transcription, translation, DNA replication... Operational genes: “housekeeping genes” for cellular processes (biosynthesis of amino acids, fatty acids, nucleotides, cell envelope proteins...) Doolittle Cold Spring Harbor Symp. 2009

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