Open questions in the origin of

Purificación López‐García Unité d'Ecologie, Systématique et Evolution CNRS & Université Paris‐Sud, France

1. Facts

2. Models

3. Testing the models

4. Open questions

The ‐ dichotomy

Edouard Chatton (1925 and 1937) Stanier & van Niel, 1962 Terms Prokaryote & Eukaryote The concept of a bacterium (autotrophic flagellated protozoa) (modern meaning) The tree of life (SSU rRNA‐based)

Prokaryotes predate eukaryotes: fossil evidence

Ga 4.6 3.8 3.5 2.1 1.5 0.55 0.002 O2 Stromatolites Microfossils Eukaryotes Isotopes Fossil lipids

Tappania plana, 1.5 Ga

Acritarchs, 1.5 Ga

Widespread fossil stromatolites in 2.7 Ga‐old Archaean rocks Prokaryotes predate eukaryotes: mitochondria

1) Mitochondria derive from endosymbiotic alphaproteobacteria

Alphaproteobacteria

Cyanobacteria

Prokaryotes predate eukaryotes : mitochondria 2) The last common ancestor of extant eukaryotes had mitochondria

Eukaryotic "crown" Mitochondria Stramenopiles Ciliates Hydrogenosomes Fungi Dinoflagellates Sporozoa Mitosomes Metazoa Rhodophyta Slime molds Plants Entamoeba Mitochondria Amoebae Euglenozoa Myxomycetes Trichomonads Trachipleistophora hominis Diplomonads Microsporidia “Archezoa”

18S rRNA Entamoeba histolytica Bacteria Sogin, 1991 Energy & Carbon Replication

metabolism Transcription

Membrane lipids Translation

Symbiosis & Evolution

A

EK

B

Genomic redundancy Increase of Change of evolutionary Compartmentation selective rate Complexity constraints Evolutionary flexibility Innovation Patterns & processes

Host

LECA

Mitochondrial ancestor

Last Eukaryotic Common Ancestor

Host

LECA

Mitochondrial ancestor

Last Eukaryotic Common Ancestor ? LECA, a complex ancestor

High metabolic flexibility & complexity Cytoskeleton Nucleus & nuclear pore complex Endocytic & exocytic pathways Complex trafficking network (Golgi, lysosomes/endosomes) Eukaryotic flagellum Proteasome Ubiquitin signaling Splicing Mitosis & cytokinesis Most likely sex (meiosis) Koonin, Cell 2010 RNA interference

Bacteria, archaea Bacteria, archaea Wickstead & Gull, JCB 2011

Host

LECA

Mitochondrial ancestor ? ‐ What kind of alphaproteobacterium? Rickettsia or Pelagibacter proposed affinities questioned ‐ Was it a facultative anaerobe? Many mitochondria scattered in the phylogenetic tree ferment (as hydrogenosomes do) or use electron

acceptors other than O2 (nitrate, nitrite, fumarate) ‐ ancestral or HGT? ? Host

LECA

Mitochondrial ancestor

The "proto‐eukaryote" or "tree of life" model

Jekely, 2003, 2005 Poole & Penny, 2006 De Duve, 2007, etc. The Neomuran hypothesis Tom Cavalier‐Smith

1 single membrane = (Gram positive bacteria + Eukaryotes) Other Gram negative bacteria Actinobacteria Eukaryotes Archaea Firmicutes

~750 Ma

mitochondria

Chloroflexi ("Chlorobacteria")

2 membranes

T. Cavalier‐Smith, Biol Direct 2006

Endomembrane system in Planctomycetes

Gemmata obscuriglobus

• Nucleus-like structure (ribosomes on both sides) • Simple form of endocytosis

PVC super-phylum Planctomycetes-Verrucomicrobia-Chlamydia

McInerney et al, BioEssays 2011 Endomembrane systems in bacteria

Betaproteobacteria Nitrosomonas + ‐ NH4 + O2 NO2 Axial filaments in Periplasmic space spiroquetes Cyanobacteria Alpha‐ & Gammaproteobacteria (methanotrophs) + CH4 + O2 CH3OH etc

Methylosinus sp. Methylococcus capsulatus Symbiosis‐based chimeric models

?

Symbiogenetic models… Serial Endosymbiotic Theory D. Searcy, 1992 The hydrogen hypothesis

Margulis 1970, 1993, 2000 Thermoplasma‐like Martin & Müller, 1998 archaeon Thermoplasma‐like Methanogenic archaeon archaeon

Spirochetes organics H2S H S0 2

CO2 CH4 Facultative anaerobic Purple bacterium alphaproteobacterium (mitochondrial H2S‐dependent photo‐ (fermentation) Cyanobacterium ancestor) or chemoautotrophic (chloroplast ancestor) proteobacterium

Martin & Koonin, 2006 Endosymbiotic origin of the nucleus: 3 symbionts CO organics 2 Syntrophy hypothesis Moreira & López‐García 1998 H López‐García & Moreira 2006 2 1st endosymbiosis: methanogenic archaeon CO 2 CH4 within fermentative (H2‐producing) myxobacterium (Deltaproteobacteria)

2nd endosymbiosis: versatile alphaproteobacterium facultative aerobe, methanotroph

Eukaryotic‐like traits in myxobacteria Specific proteins: •Serine‐threonine & tyrosine kinases Phylogenomics: at least some genes were ancestrally • Calmodulin‐type morphogenesis protein transferred from myxobacteria to eukaryotes: fatty •17 b‐hydroxysteroid dehydrogenase acid  oxidation pathway • Ras/Rab/Rho‐type small GTPases Schluter, Ruiz‐Trillo & Pujol, 2011 •High mobility group (Y‐type) proteins •Reverse transcriptase (and retron elements) General processes: •Synthesisof sterols • Phosphatidyl‐inositol cycle •Participation of G‐proteins in signal transduction •Synthesisof antibiotics (many against eukaryotes) •Synthesisof melanin •Predation: protein‐digesting machineries (periplasm)

Large genomes, e.g. Myxococcus xanthus (9.14 Mb): >1500 selective specific duplications: • cell‐cell signaling • small molecule signaling • integrative transcription control Origin of mitochondria  origin of eukaryotes 2 symbionts

Various subsequent models to hydrogen hypothesis: ‐ In general, no clear metabolic or other driving force advanced (idem for nucleus) ‐ Based on protein/gene content & phylogenetic analyses ‐ Based on cell biology: potential to develop endomembranes

Membrane remodeling in archaea

Periplasmic vesicles Budding

Ignicoccus hospitalis and its symbiont (parasite?) Nanoarchaeum equitans

Chemolithoautotroph reducing S° to H2S T opt ~90°C

Ignicoccus on the road to eukaryotes, van Oijn NRM 2010 Nanoarchaeum‐like organism as endosymbiotic nucleus in Ignicoccus‐like ancestor. J. Godde, J Cell Biosci 2012 as archaeal ancestor?

Schleper & Wagner, 2011

TACK superphylum

Guy & Ettema, TiM 2011

A stem archaeal ancestor as host? Cell division & vesicle formation in archaea

ESCRT‐III

Makarova, Yutin, Bell & Koonin, Nat Rev Microbiol 2010 Can we test these models?

Endosymbiotic origin of Proto‐eukaryotic lineage 2 symbionts nucleus (3 symbionts)

Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Archaeal‐like Archaeal‐like Archaeal‐like 2nd bacterium (e.g. myxobacteria)

Phylogenomics: difficulties • Mitochondrial and chloroplast ancestry easily retrieved because: ‐ More recent ‐ Conservation of function • Symbiotic ancestors of mitochondrial host difficult (impossible?) to identify because: ‐ Ancient event: maybe no (discriminating) phylogenetic signal kept ‐ (Drastic) change of function & innovations ‐ Acceleration of evolutionary rate

Conflicting results, phylogenomic impasse?

Gribaldo et al., Nature Reviews Microbiology, 2010 Current favoured model

The hydrogen hypothesis & alike Archaeal host establishes symbiosis with the alphaproteobacterial ancestor of mitochondria

Need for detailed mechanistic process

… the devil is in the details!

How did the nucleus evolve?

Selective forces proposed for the emergence of the nucleus in 3D models: •T. Cavalier‐Smith (1987): to prevent chromosome shearing by cytoskeletal movements •G. Jékely (2008): to prevent the formation of chimeric ribosomes in a proto‐eukaryote devoid of nucleus after engulfment of mitochondria

Primary secretory role of endomembrane system ‐ Small GTPases: Sar1, Arf, SRb, Ran, Rab, Ras, Rho

G. Jekely, 2003 & 2005 Selective forces for the origin of the nucleus Hydrogen hypothesis Syntrophy hypothesis

2) Ex‐aptation of pre‐existing membrane to prevent chimeric protein synthesis due to intron spreading

De novo nuclear membrane O2 respiration to prevent chimeric protein synthesis due to intron spreading loss of methanogenesis & archaeal membrane

organics CO2

H2 H2

CO 2 CH4 CH4 1) Secretory endomembrane organics system: transport of hydrolytic enzymes to periplasm

The problem of the membranes Bacteria Archaea Eukaryotes

Koonin & Martin, TiG 2005

KogaKoga et etal., al, JME 1998 1998

Lombard, Lopez‐Garcia & Moreira, NRM 2012 The problem of the membranes Hydrogen hypothesis Syntrophy hypothesis

(& other H0 where (& other H0 where archaeon = host) archaeon = endosymbiont)

Conclusions

• Models on the origin of eukaryotes: we need the details! plausible processes to account for observed phylogenetic patterns

Major problems: ‐ Origin of the nucleus unresolved (no clear selective forces) ‐ Nature of membranes unexplained in currently favoured endosymbiotic models (archaeon engulfs mitochondrial ancestor) [the possibility of an endosymbiotic origin of the nucleus needs to be considered]

• Phylogenomic analyses might help to discriminate between/formulate new plausible models ‐ Better eukaryotic (protist) sampling: LECA portrait More genomes… ‐ Better prokaryotic (B/A) sampling & explore NATURE!

• Perhaps we will never know: contingent event Cпасибо Thank you