Eukaryotic Cell Biology And The Tree Of Life Flashcards
Structure
- Carl Woese (ribosomes, methodology, archaea)
- Super Tree Analysis
- Reconstructing LECA
- ESGs
- Early eukaryotes
Carl Woese
used rRNA genes to calculate the tree of life
What do you need to calculate the tree?
- a universal gene
- mixture of evolutionary rates
- easy to sequence
rRNA genes
- lots! doesn’t need PCR to amplify
- extract and run on gel
Ribosomes
- RNA + proteins
- drive translation
- large subunit guide tRNA
- small subunit is mRNA BS
Methodology
1) incubate cell cultures with 32-P
2) extract RNA
3) run 2D gel electrophoresis
4) expose gel to photo film
5) interpret fringerprint to characterise rRNA gene sequence
6) compare sequences using distance measurements
7) calculate Tree of Life
32-P
Incorporated into Dna
Photo film
- radioactive RNA Fragments mark the film; generates a map/fingerprint
Interpret
Annotate
What did ssu rRNA reveal?
Archaea ; 3D tree
3D Tree
- assumed rooted tree
- interpretation caution requiref
Archaea
- extreme + mesophyllic (marine water column [Nitrosopumilis maritimus] and soil [Nitrosodphaera virnnensis])
ssu rRNA gene advantages
- ds/ss regions determine 2• structure
- range of evolution rates; correspond to rRNA 2• structure
- helpful for resolution + taxon-specific PCR primers
- conserved
ssu rRNA gene disadvantages
• phylogenies subject to LBA
LBA
makes groups with fast rRNA evolution (Microsporidia, amitochondriates), appear as deep eukaryotic branches
Partial LBA control?
1) concatenation ssu and lsu rRNA alignments w/ models that account for heterogenous sequence evolution
2) concatenation with 45 protein sequence alignments
Partial LBA control reveals…
2D model
2D
- Eukaryotes evolved from within the archaea
- archaea: eukaryotic progenitor cellular chassis
Super Tree Analysis
- calculates trees independently, one gene family at a time; no concatenation
- forms a matrix of relationships
- calculates “best” tree
Adding eukaryotes to the prokaryotic super tree analysis reveals…
1) within the Cyanobacteria; relic of plastic endosymbiosis
2) [strip all genes w Cyanobacteria sisterhood]
3) α-proteobactetia; relic of mitochondrial endosymbiosis
4) [strip]
5) 2D!
Questions after Sta?
1) 7.4% γ-proteobacterial
2) 4.9% spirochaetes
- alternative signal/input?
- noise?
Situation after STA
- 13.9% archaea
- 10.8% α-proteobacterial
- 21% cyanobacterial
- 54% unresolved bacteria-like
- Ring!
Reconstructing LECA
1) compare extant taxa, looking for similar gene families/ cellular features
2) verify vertical trait evolution between gene and cellular trait (no HGT)
3) map to resolved species tree
LECA
- Complex eukaryotic cell, much like extant heterotrophic protist
- sophisticated, highly derived organellar system
- 23 Rab GTPAses
LECA chimaera
1) bacterial cell membrane
2) mitochondrial genome
3) archael MCMs
4) archael histone-bound chromatin
5) archael ribosomes
Bacterial + organelles cell membrane
- D-glycerol ester
- unbranched fatty acid chains
- sn-glycerol-3-phosphate (G3P)
Archael cell membrane
- L-glycerol ether
- branched isoprenoid chains
- sn-glycerol-1-phosphate (G1P)
α-proteobacterial derived mitochondrial genome
- circular
- nuclear encoded, mitochondrial/cytoplasmic localised proteome
- mitogenome + ribosome
- ETC proteins
Archaea as part of the chimera
- informational functions
- lower HGT
- ^ protein protein interactions
- ^ expression
- conditional essentiality for viability under KO
- nuclear, DNA management
FECA -> LECA
gene duplication
MCMS
- Archaea: homohexamer
- Eukaryotes: heterohexamer
- essential universal condition
Histone-bound chromatin
- homologous
- Archaea: 3 dimers wrap c90bp DNA
- Eukaryotes: heterohexamer wraps 146bp
Ribosomes
- structural similarity
- all archael r-proteins are represented in Eukaryotes
- no crossover in r-proteins between Archaea and Bacteria
ESPs
De novo acquisition
1) cytoskeleton components
2) ribosome proteins
3) EM
4) signalling
EM
- maintains eukaryotic organellar systems via subcellular targeting mechanisms
- co-operative action of multiple paralog-rich protein families
EM Families
- SNARES
- Rab GTPases
- ensure specificity and fusion of carriers and targets
Tubulin cytoskeleton
- diversified ESPs
- numerous rounds of gene duplication
- kinesin, myosin
Dacks model
- Gene duplication, and multiple specificity-encoding proteins drives increased organellar complexity
- single primordial EM compartment differentiates into an array of organelles
Myosin-Actin cytoskeleton
- protein domain recombination * gene duplication
Early Eukaryotes
- intron invasion and expansion facilitates protein domain recombination via alternative splicing
- functional network complexity ^
- gene architecture modularity ^
Duplication
- gene innovation through architecture recombination
- ^ gene dosage
- neo- and subfunctonalisation
