4. Early times

1. 4. Early times What is life? Reproduction Energy transfer Metabolism Growth Life Homeostasis Evolution The ability to evolve is an essential feature of life A self replicating robot

2. Three domains of life Terrestrial forms Cyanobacteria Deinococcus radiodurans Actinobacteria Proteobacteria SalmonellaEnterobacteriumPseudomonasHelicobacterRickettsia Cell wall Gram positive Firmicutes MycoplasmaBacillusStaphylococcusStreptococcusActinobacterium Spirochaetales 2800-3100 Mya Euryarcheota MethanobacterialesThermoplasmalesThermococcalesMethanococcales ThermotogalesAquifex 3500-3700 Mya Thermophiles Mostly extremophiles 3800-4000 Mya 3800-4100 Mya Crenarcheota SulfolobalesDesulforococcales Mitochondria, Nucleus, 9+2 cilia, cytoskeleton,meiosis 2000-2700 Mya Root Nanoarcheota Nanoarchaeum Eukaryota

3. Did life evolved once? uses only L-optical isomeres of amino acids uses the same 20 standard amino acids uses the same 4 nucleotids has appr. 20% of genes in common. These represent the genes of basic cell metabolism.

4. But The detailed mechanics of DNA replication are very different between Archaea and Eubacteria. Many biochemical pathways are catalysed by non-homologous enzymes. Today’s basic energy pathway, fermentation, evolved twice in Archaea and Eubacteria. Cell membranes and cell walls are non-homologous in Archaea and Eubacteria. Archaea and Eubacteria probably emerged twice.

5. Some older theories Primordial soup Stanley A. Miller (1930-2007) Alexandr Oparin (1894-1980) Hypercycles The hypercycle theory starts with lipid bubbles (coacervates) and replicators that generate proteins that assemble other replicators in a cycle. Manfred Eigen(1927- holds that live first originated in stellar clouds (maybe by using radioactivity as energy source as found in deep (3 km) rocks on earth: low diversity Archean communities). Comets broad life to earth. Panspermia

6. The origin of life Günther Wächtershäuser (1930- Micheal Russel Bill Martin (1957- The recent mainstream theory sees basic biochemical reactions prior to the evolution of replicators.and cell membranes. First organisms were part of rock surfaces structures • Prebiotic conditions in a medium hot environment powered by a temperature and pH gradient resulted in the creation of the necessary biomolecules (monomers). • Polymerization of nucleotides resulted in first random replicating RNA that served also as enzyme. • Polymers became enclosed in lipid layers. • Evolution set in. Proteins outcompeted ribozymes in catalytic ability.

7. The distribution of hydrothermal vents on earth Fornay and Shank, Woods Hole At Lost City a main process of H2 production is serpentinization of Olivine: 6(Mg1.5,Fe0.5)2 SiO4 + 7H2O → 3[Mg3Si2O5(OH)4] + Fe3O4 + H2 Hydrogen Magnetit Serpentine Water Olivine

8. Black hydrothermal smokers have core temperatures > 300° C. Tube worms (Pogonophora) Cooling deep sea volcanoes From Martin et al. 2008 Deep-sea hydrothermal vents support extraordinary diverseecosystems. These are the only communities on Earth whose immediate energy source is not sunlight.

9. Lost city Alkaline hydrothermal smokers with core temperatures from 50 to 150° C. A field of alkaline low temperature deep sea smokers discovered in 2000. 60 smokers, 10-60 m high. Carbonate covered. Inorganic methane and H2 production. Fe, S-microbubbles in a Lost City smoker. Water percolates upward through the bubbles. Black smokers Alkaline smokers Found on all spreading centers Fueled by cooling volcanoes Temperatures >300 C° Fluids are enriched in CO2, H2S, CH4, H2+metals pH 2-5 Supports dense and diverse macro-faunal and microbial communities Along slow-spreading systems. Volcanic heat not required Exothermic mantle temperatures <150° C. Fluids are enriched in CH4, H2, few metals & S pH 9-11 Support diverse microbial communities, sparse macrofauna?

10. The alkaline smoker system Water percolates upward forming small bubbles Water percolates downward into newly formed rocks 50 ° C – 100° C Olivine (Magnesium Iron Silicate) and other minerals FeS + H2S → FeS2 + H2 DG = -38.4 kJmol-1 Exergonic reraction H2, N2, H2O, NH3, CO2, H2S Percolation of water within a temperature gradient Serpentinization Iron sulphurbubbles Hydrogen, sulphids 100 ° C – 200° C Upward flows from the upper mantle Several hundred meters

11. Water percolates upward forming small bubbles 50 ° C – 100° C Steadyproduction of acetyl - thioesters Iron sulphurbubbles Iron–sulphurmineralscatalyzethesereactions Percolation of water within a temperature gradient DG = -121.3 kJmol-1 Exergonic reaction H2 + CO2 + H2S → CH3SH + H2O H2 + CO2 → CH4, CH3COOH, HCOOH 100 ° C – 200° C Abiotic hydrocarbonate productionProskurowski G. et al. 2008 CO2aq + H2 → CnHm + H2O Iron-sulphur catalysts are still found at the heart of many proteins today. For instance Nitrogenase contains as active catalytic centre Iron-Molybdenum-Sulfur)

12. Water percolates upward forming small bubbles pH < 5 50° C – 100° C Accumulationinbubblesatlowertemperatures Iron sulphurbubbles Percolation of water within a temperature gradient Aminoacid and nucleotidformationalongthegradients Alkaline hydrothermal vents Acetylphosphate-, Pyrophosphateact as energy stores 100° C – 200° C pH > 9 The electrochemical gradient between the alkaline vent fluid and the acidic seawater leads to the spontaneous formation of acetyl phosphate and pyrophospate, which act just like adenosine triphosphate or ATP, the chemical that powers living cells. These molecules drove the formation of amino acids and nucleotides Thermal currents and diffusion within the vent pores concentrated larger molecules like nucleotides, driving the formation of RNA and DNA. Early life started as an inverse PCA machine.

13. The RNA world Current life needs the interplay of DNA for reproduction and proteins for metabolism RNA is able to replicate and to catalyze biochemical reactions (ligating and peptide bonding) Water percolates upward forming small bubbles Eucaryotic RNaseP ribozyme pH < 7 50° C – 100° C Biochemicalcyclesdifferinstability Evolutionsetsin Iron sulphurbubbles Percolation of water within a temperature gradient Alkaline hydrothermal vents Selfreplicatingcatalyticoligonucleotids Nucleotidformationalonggradientscatalyzed by iron-sulphurminerals 100° C – 200° C pH > 7

14. First fatty proto-cell membranes Water percolates upwoard forming small bubbles pH < 7 50 ° C – 100° C Bubblegetscoated by fattymolecules Iron sulphurbubbles Percolation of water within a temperature gradient Bubblegetscoated by fattymolecules Alkanline hydrothermal vents Bubblegetscoated by fattymolecules 100 ° C – 200° C pH > 7 Some protocells started using ATP as well as acetyl phosphate and pyrophosphate. The production of ATP using energy from the electrochemical gradient is perfected with the evolution of the enzyme ATP synthetase, found within all life today. Proto-cell like vesicles made of fatty acids form spontaneously and encapsulate nucleotids. Budin et al. 2009.

15. Two origins of prokaryotes H2 Proton pump (Chemiosmosis) Iron sulphurbubbles Iron sulphurbubbles H2 H2 Proton pump 4H2 + CO2 → CH4 + 2H2O 4H2 + 2CO2 → CH3COOH + 2H2O e- e- e- e- H2 Methanogenesis Acetogenesis Once protocells could generate their own electrochemical gradient through chemiosmosis, they were no longer tied to the vents. Cells left the vents on two separate occasions. This marks the beginning of life. ATP ATP Archaea Eubacteria Own energy production Own energy production Eukaryota

16. Energy gradient Standard chemical reactions driven by electrochemical gradients Within hydrothermal vents Problems First metabolicpathways, Co-factors RNA –DNA interplay? Oligonucleotids and proteins need chiral monomers. Replicators, Enzymes Generation of autonomous electrochemical gradients Differentialsurvival Differentialsurvival Because all bubbles eventually decay differential survival does not mean differential proliferation of autonomous cycles. Autonomous chemical cycles Homeostasis Homeostasis How long do bubbles survive? Reproduction Reproduction No replicator transfer between bubbles. All has to be within one lucky bubble? The question of time. Outside hydrothermal vents Full onset of evolutionary process Differentialreproductionrates Differentialreproductionrates If fast evolution to life why only two primordial domains? Or do more exist? Full life in common sense Growth Growth

17. Life started at higher temperatures Reconstruction of thermooptima of ancient enzymes The archaean strain 121 grows at 121°C. Gouy, Chaussidon. 2008. Nature 451: 635

18. Nanons („nanobacteria”) Calcifying nanoparticles – carbonate precipitates First identified as causing kidney stones (1988) by Kajander and Ciftioglu. They are possibly involved in biomineralization. This is the formation of inorganic crystalline structures in association with biological macromolecules. This process is also referred to as calcification. Nanons have „cell” walls. They replicate autonomously and grow. They do not contain nucleotids. It is highly controversial whether these particles are alive. Probably they are self replicating mineral complexes. Nanobacteria in limestone

19. Nanobes Nanobes are filament like structures that are 20 to 150 nm in diameter. They were found in 3 km depth in Australia at temperatures of app. 150ºC. They are made of Carbon, Oxygen and Nitrogen. They grow at aerobic conditions. Perhaps they are only organic crystals that grow like „normal” inorganic crystals. The Martian meteorite ALH 84001 Whether they are a new form of living organisms is still highly controversial.

20. Nanobesfrom Austrian thermal springs Thermal springsrepresent a part of a water-circulating process forming a temperature gradient. Long filaments Nanobes form biofilms Single Nanobes Nested filaments The way of self assembly Heinen et al. 2007

21. Replication and error thresholds Genome sizes decline during selection. The length N of simple RNA replicator’s (the information content of a proto genome) is defined by the Eigen equation Manfred Eigen(1927- s: a measure of selective superiority (fitness) p: the mean probability of correct replication of a nucleotide 1-p is therefore the error rate Early replicator systems with high copying error rates had only limited information content

22. The oldest remains of life Stromatolites from the Gunflint Formation, Ontario, Canada 1900 Mya are remains of Cyanobacteria Oldest known sure eucaryotes (chlorophytes) from San Berhardino, California having 1400 Mya. Archaeoscillatoriopsis maxima Marble Bar in Western Australia 3500 Mya. It might be a Cyanobacterium Bacterium from Western Australia, 3500 Mya. Again it might be a Cyanobacterium

23. A major invention: Endosymbiosis Mitochondrion Chloroplasts Lynn Margulis (1938-) Zooxanthellae within hermatypic corals and giant clams Cyanobacteria

24. Evidence for the endosymbiont hypothesis • Both mitochondria and plastids contain DNA is similar to that of bacteria. • They are surrounded by two or more membranes similar to prokaryotic cell membrane. • New mitochondria and plastids are formed only through a process similar to binary fission. • Phylogenetic estimates constructed with bacteria, plastids, and eukaryotic genomes suggest that plastids are most closely related to cyanobacteria. • Some proteins encoded in the nucleus are transported to the organelle, and both mitochondria and plastids have small genomes compared to bacteria. • Among the eukaryotes that acquired their plastids directly from bacteria (known as Primoplantae), the (glaucophytes) algae have chloroplasts that most strongly resemble cyanobacteria. • Proteins of organelle origin use N-formylmethionine as the initiating amino acid. Possible further endosybionts that triggered the evolution of eukaryotes: Centrioles and kinetosomes Peroxysomes Nucleus

25. The rise of the oxygen level First Eucaryotes First metazoa Cyanobacteria After Anbar (2008) and Frey et al. (2009) • Why did oxygen levels increase? • Plate tectonic changed the demands of oxygen to react with volcanic lava • Cyanobacteria invented photosynthesis • Effective photosynthesis of cyanobacteria within first eucaryotes

26. A major invention: Sex Sexual reproduction refers to the union (syngamy) of two genomes followed later by genome segregation (reduction). Sexual reproduction nearly always includes recombination that is the reshuffling of alleles. In principle sex is disadvantageous because • Asexual populations reproduce faster • Recombination destroys advantageous allele combinations • Sexual reproduction needs investment in gamete production and growth Sexual Asexual Sexual reproduction is an autapomorphy of all eukaryotes Many eukaryote lineages returned to asexual reproduction Most asexual (parthenogenetic) species are phylogenetically young. Bdelloid Rotifera are an exception and pose a theoretical problem. Taraxacum spec. Rotifera Andricus spec.

27. Why sex? Muller’s ratchet In an asexual species deleterious mutations might increase over time. The frequency of individuals without deleterious mutations decreases. In a sexual population recombination increases the frequency of the zero mutation class. The decline in fitness by Muller’s ratchet is relatively slow. It is unknown whether the effect can counterbalance the costs of sexual reproduction

28. Why sex? Adaptation to changing environments Sexual species Asexual species Sex generates additional genetic variability. The adaptational advantage might counterbalance the costs of sex F1 A B C F1 A B C Mutation F2 AB AC BC F2 AA BB BC DNA repair during meiosis Syngamy allows for DNA repair and therefore reduced replication error probabilities. According to the Eigen equation this allows for larger genome size. DNA glycosylase AP endonuclease DNA polymerase 1 DNA ligase

29. The basic tree of eukaryotic life Rhodophytes Vascular plants Chlorophytes Glaucophytes Chromalveolatae („Diatomea”, „Ciliatae”) Chloroplasts Discicristates(„Euglenoidea”) Myxomycetes 1.6-1.8 mya 1.0-1.6 mya Metazoa 0.8-1.5 gya Choanoflagellates Excavates(„Flagellata”, „Amoeba”) Cercozoa(„Foraminifera”) NucleusSex Fungi Mitochondria Root 2.0-2.7 gya

30. Cavalier-Smith 2002, 2003 Chromalveolata Plantae The basic tree of eukaryotic life Contains many paraphyletic groups (grades) Chromista Alveolata Endosymbionts Plastids Archezoa Discicristata Metazoa Excavata Porifera Lamblia Euglena Choanozoa Eumycota Heliozoa Cercozoa Rhizaria Rhizopoda Heliozoa Saccharomyces Opisthokonta Apusozoa Why are there no early evolutionary stages of eucaryotes? The problem of missing links. Bikonta 2 cilia Mycetozoa Unikonta 1 cilium,Nucleus, Cytoskeleton, 80 S Ribosomes, Peroxysomes Mitochondrium Archamoeba Lobosa Slime mold Root (2.0-2.7 Gya) Amoebozoa Arcella Ancyromonas

31. Today’s reading Life on Earth: http://www.cbs.dtu.dk/staff/dave/roanoke/bio101.html http://www.cbs.dtu.dk/staff/dave/roanoke/bio101ch19a.htm Lane N. 2009. Was our oldest ancestor a proton powered rock. New Scientist 270. Martin W., Baross J., Kelley D., Russell M. J. 2008. Hydrothermal vents and the origin of life. Nature Reviews Microbiology 6: 805-814. Martin W., Russell M. J. 2007. On the origin of biochemistry at an alkaline hydrothermal vent. Phil.Trans R. Soc Lond. B. 362: 1887-1926. Eucaryote origins: http://www.bact.wisc.edu/themicrobialworld/origins.htmlhttp://ijs.sgmjournals.org/cgi/content/abstract/52/2/297 Evolution of sex: http://en.wikipedia.org/wiki/Evolution_of_sex Recombination: http://www.blackwellpublishing.com/trun/artwork/Animations/Recombination/recombination.html Meiosis: http://www.johnkyrk.com/meiosis.html Molecular timescale of evolution in the Proterozoic: http://evo.bio.psu.edu/hedgeslab/Publications/PDF-files/182.pdf The origin of metazoa and the fossil record:http://www.bionet.nsc.ru/live/ppt/Fedonkin_2003.pdf