THE PROKARYOTES

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

Zuckerkandl and Pauling

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

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).

Eubacteria

>9 KingdomsSame type of ribosomesPolysaccharide of outer wall made of MureinMost groups involved in global nutrient cyclingMany of economic importanceDiseaseOther 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. 2013Using 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

Forterre 2015pg=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

Figure 3. Schematic universal tree updated from Woese et al. (1990)

Three Domains

Eukaryotes Early

Eocyte

Ring of Life

Modified from McInerney et al. 2015

Argued that the domain concept was indefensible because eukaryotes are not monophyletic unless we consider all 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