RECONSTRUCTING A “UNIVERSAL TREE”
Classical view
Prokaryotes Eukaryotes
1977: C. Woese
3 “primordial kingdoms” (or domains)
- based on ribosomal RNA sequence comparisons
All living things share same common ancestor
BacteriaArchaea
Eucarya
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
University of IllinoisCarl Woese (1928-2012) “… famous for defining the Archaea (a new domain or kingdom of life)”
1989: Iwabe - rooting the universal tree
- if set of duplicated genes is present in all 3 lineages,
- can use one gene (eg. Gene A2) as an outgroup when comparing the other one (Gene A1) in all 3 lineages
Fig. 5.40
then duplication must have occurred in their common ancestor
Fig. 5.41
- Translational elongation factors EF-G and EF-Tu are homologousand both genes are present in all life forms
… so ancient duplication prior to divergence of 3 superkingdoms
Bacterial lineage diverged prior to archaeal & eukaryotic ones
Plant-animal-fungal trichotomy
Fig. 5.39
Where would you place the root on this tree?
Bacteria
Archaea
Eucarya
Maximum parsimony analysis of – 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 diversedata sets support a sister-group relationship between animals and fungi.”
Baldauf & Palmer PNAS 90:11558, 1993
ENDOSYMBIOTIC ORIGIN OF ORGANELLES
1910 - Mereschkowsky – morphological similarities betweenchloroplasts/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 forendosymbiotic origin, from ribosomal RNA data
eg. chloroplast & cyanobacterial sequences are more similar thaneither is to nuclear homologue….
Gray PNAS 86: 2267, 1989
Phylogenetic tree based onSSU ribosomal RNA data
chloroplast
mitochondrial
How do you interpret thedata in this figure?
Dot = divergence point of -proteobacterial and mitochondrial lineages
And certain of them (a few? lineages) lack mitochondria Fig. 5.39
Protists are very diverse unicellular eukaryotes
Tree based on ribosomal RNA data
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
mitosomeNature 426: 172, 2003
Alberts Fig. 14-56
Evolutionary pathway fororigin of eukaryotic cell
Many genes transferred to nucleus
& others lost
… a few retained inorganelle
What features of this figure are out of date?
Fig. 5.43
Certain genes for DNA replication/repair, transcription/translation…shared by archaea & eukaryotes (but absent in bacteria)
Chimeric nature of eukaryotic nuclear genomes
Possible explanations:
1. Eukaryotic ancestor - archaeal, but bacterial-type genes acquiredthrough horizontal transfer- from organelles (bacterial endosymbiotic origin)
- more recent direct transfer from bacteria2. Eukaryotic ancestor - chimeric fusion of bacterial & archaeal-type
genomes
Eukaryotic genomes have bacterial-type and archaeal-type genes
Martin & Koonin Nature 44:41, 2006
Model for origin of nucleus-cytosol compartmentalization “in the wake of mitochondrial origin”
HORIZONTAL GENE TRANSFER (p. 359-366)
- lateral transfer of genetic information from one genome to another (eg. between two species)
Mechanisms:
1. 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)
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
A B C A B C
True tree Inferred tree Fig. 7.22
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 beco-ordinately regulated (operon)
4. Acquisition may re-define ecological niche of microbe
and Doolittle Science 284: 2124, 1999
“Web-of-life”
How rampant was (is) lateral gene transfer - especially among microbes?
Was early cellular life communal?
“Highways of gene sharing” among prokaryotes?
Transposable elements carry along “foreign genes?”
www.whoi.edu/cms/images/oceanus/2005/4/v43n2-teske_edwards1en_8591.gif
Doolittle “Uprooting the tree of life” Sci.Amer. 282:90, 2000
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