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

Lane & Archibald Trends Ecol Ecol 23:268, 2008

“Six hypothesized supergroups of eukaryotes”

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….

Fig. 5.45

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

Brown Nat Rev Genet 4:121, 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

Operational genes: “housekeeping genes” for cellular processes (biosynthesis of amino acids, fatty acids, nucleotides, cell envelope proteins...)

Informational genes: machinery for transcription, translation, DNA replication...

Doolittle Cold Spring Harbor Symp. 2009