1. Domains & Dogma

2. Systematics of Prokaryotes
Focus on animals and plants
History limited to 20% of evolutionary time
How to classify
prokaryotes?
Limited in
morphological
characters

3. Gram Stain and Structure

4. rRNA unlocks the domains
Emile Zuckerkandl ( ); Austria & USA. Molecular biology and molecular clock
Linus Carl Pauling ( ) USA Founder of fields like quantum chemistry and molecular biology
Suggested that a tree of life might be generated by comparing sequences of biopolymers like RNA
Zuckerkandl and Pauling

5. Ribosomal Structure
Two subunits

6. Ribosomal subunits= rRNA molecules + proteins

7. Prokaryotes Eukaryotes

8. What’s the ‘S’?
Svedberg units: a measure of how quickly particles sediment in an ultracentrifuge

9. What’s the ‘S’?
Svedberg units: a measure of how quickly particles sediment in an ultracentrifuge
Larger the particle, the greater its S value
Smaller subunit of a ribosome sinks slower than the larger subunit

10. Why then does 5S + 23S = 50S?

11. Why then does 5S + 23S = 50S? Shape AND size determine sedimentation rate…

12. Ribosomal RNA Molecules
Components of the ribosomes of ALL ORGANISMS
Changes in rRNA nucleotide sequence indicative of evolutionary history
SSU rRNA

13. Carl Richard Woese
, USA; Developed system based on 16S rRNA in 1977

14. Carl Woese and George Fox 1977

15. A modification of Woese et al. (1990) from Brock et al. (1994).

16. The system we propose here will repair the damage that has been the unavoidable consequence of constructing taxonomic systems in ignorance of the likely course of microbial evolution, and on the basis of flawed premises (that life is dichotomously organized; that negative characteristics can define meaningful taxonomies).
- Carl R. Woese, Otto Kandler, and Mark L. Wheelis Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences. USA. 87:

17. Eubacteria >9 Kingdoms Same type of ribosomes
Polysaccharide of outer wall made of Murein
Most groups involved in global nutrient cycling
Many of economic importance
Disease
Other functions (e.g. antibiotic producers)

18. Archaea Differ from the Eubacteria Form of ribosomes No murein
Different lipids
Different RNA polymerase

19. Two different supertrees generated by ML methods for complete genomes of 45 taxa. Daubin et al. 2002

20. Ciniglia et al. 2004

21. Lang et al. 2013
Using 24 genes and 3000 taxa

22. Raymann et al. 2015
Support for a two- domain system. Eukayotes arose from within the Archaea and sister to the Lokiarchaeota.

23. Spang et al. 2015
Colored dots indicate distribution of Eukaryotic Signature Proteins

24. pg=peptidoglycan
LUCA=Last universal common ancestor
LBCA=Last bacterial common ancestor
LACA=Last archaeal common ancestor
LARCA=Last Arkarya common ancestor
FME=First mitochondriate eukaryote
LECA=Last eukaryotic common ancestor
SARP=Stramenopiles, alveolates, rhizobians, plantae
Forterre 2015
Figure 3. Schematic universal tree updated from Woese et al. (1990)

25. Impact of Horizontal Gene Transfer on the tree of life
Ford Doolittle, b. 1942
Dalhousie University
Figure 3 from Doolittle (1999)

26. HGT and Ribosome Splitting Factor (HflX)
From Suswastika et al. (2014)

27. Modified from McInerney et al. 2015 Three Domains Eukaryotes Early
Argued that the domain concept was indefensible because eukaryotes are not monophyletic unless we consider all of life
Eocyte
Ring of Life

28. Life’s history is complex and we should not try to simplify it to suit our need for orderly nomenclatural systems. -McInerney et al. 2015