Domains & Dogma

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

Gram Stain and Structure

rRNA unlocks the domains Emile Zuckerkandl (1922-2013); Austria & USA. Molecular biology and molecular clock Linus Carl Pauling (1901-1994) 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

Ribosomal Structure Two subunits

Ribosomal subunits= rRNA molecules + proteins

Prokaryotes Eukaryotes

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

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

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

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

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

Carl Richard Woese 1928-2012, USA; Developed system based on 16S rRNA in 1977

Carl Woese and George Fox 1977

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

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. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences. USA. 87: 4576-4579.

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)

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

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

Ciniglia et al. 2004

Lang et al. 2013 Using 24 genes and 3000 taxa

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

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

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)

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

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

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

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