Transcript Slajd 1
4. Early times What is life? Reproduction Energy transfer Metabolism Growth Life Homeostasis A self replicating robot Evolution The ability to evolve is an essential feature of life Three domains of life Terrestrial forms Cyanobacteria Deinococcus radiodurans Actinobacteria Proteobacteria Salmonella Enterobacterium Pseudomonas Helicobacter Rickettsia Cell wall Gram positive Firmicutes Spirochaetales 2800-3100 Mya Euryarcheota Methanobacteriales Thermoplasmales Thermococcales Methanococcales Crenarcheota Sulfolobales Desulforococcales Thermotogales Aquifex 3500-3700 Mya Mostly extremophiles Nanoarcheota Nanoarchaeum Mycoplasma Bacillus Staphylococcus Streptococcus Actinobacterium Thermophiles 3800-4000 Mya Mitochondria, Nucleus, 9+2 cilia, cytoskeleton, meiosis 3800-4100 Mya 2000-2700 Mya Eukaryota Root 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. 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. Some older theories Primordial soup Stanley A. Miller (1930-2007) Hypercycles E1 RNA2 E2 RNA1 RNA3 E5 RNA5 E3 RNA4 E4 Alexandr Oparin (1894-1980) The hypercycle theory starts with lipid bubbles (coacervates) and replicators that generate proteins that assemble other replicators in a cycle. Manfred Eigen (1927- Panspermia 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. 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 1. Prebiotic conditions in a medium hot environment powered by a temperature and pH gradient resulted in the creation of the necessary biomolecules (monomers). 2. Polymerization of nucleotides resulted in first random replicating RNA that served also as enzyme. 3. Polymers became enclosed in lipid layers. 4. Evolution set in. Proteins outcompeted ribozymes in catalytic ability. 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 Magnetit Hydrogen Serpentine Water Olivine 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 diverse ecosystems . These are the only communities on Earth whose immediate energy source is not sunlight. 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. Alkaline smokers 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? Black 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 The alkaline smoker system Water percolates downward into newly formed rocks Olivine (Magnesium Iron Silicate) and other minerals Water percolates upward forming small bubbles H2, N2, H2O, NH3, CO2, H2S Serpentinization Hydrogen, sulphids Iron sulphur bubbles 50 ° C – 100° C FeS + H2S → FeS2 + H2 DG = -38.4 kJmol-1 Exergonic reraction Percolation of water within a temperature gradient 100 ° C – 200° C Upward flows from the upper mantle Several hundred meters Water percolates upward forming small bubbles 50 ° C – 100° C Steady production of acetyl - thioesters DG = -121.3 kJmol-1 Exergonic reaction Iron–sulphur minerals catalyze these reactions Iron sulphur bubbles H2 + CO2 + H2S → CH3SH + H2O H2 + CO2 → CH4, CH3COOH, HCOOH CO2aq + H2 → CnHm + H2O Percolation of water within a temperature gradient 100 ° C – 200° C Abiotic hydrocarbonate production Proskurowski G. et al. 2008 Iron-sulphur catalysts are still found at the heart of many proteins today. For instance Nitrogenase contains as active catalytic centre Iron-Molybdenum-Sulfur) Water percolates upward forming small bubbles pH < 5 Alkaline hydrothermal vents pH > 9 Accumulation in bubbles at lower temperatures Aminoacid and nucleotid formation along the gradients Acetylphosphate-, Pyrophosphate act as energy stores 50° C – 100° C Iron sulphur bubbles Percolation of water within a temperature gradient 100° C – 200° C 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. 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 pH < 7 Alkaline hydrothermal vents pH > 7 Biochemical cycles differ in stability Evolution sets in Eucaryotic RNaseP ribozyme 50° C – 100° C Iron sulphur bubbles Self replicating catalytic oligonucleotids Nucleotid formation along gradients catalyzed by iron-sulphur minerals Percolation of water within a temperature gradient 100° C – 200° C First fatty proto-cell membranes Water percolates upwoard forming small bubbles 50 ° C – 100° C pH < 7 Bubble gets coated by fatty molecules Alkanline hydrothermal vents pH > 7 Iron sulphur bubbles Bubble gets coated by fatty molecules Bubble gets coated by fatty molecules Percolation of water within a temperature gradient 100 ° C – 200° C 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. Two origins of prokaryotes H2 Proton pump (Chemiosmosis) e- Iron sulphur bubbles Proton pump H2 H2 e- e- 4H2 + 2CO2 → 4H2 + CO2 → CH3COOH + 2H2O CH4 + 2H2O Iron sulphur bubbles e- H2 Methanogenesis Acetogenesis Once protocells could generate their own electrochemical gradient through chemiosmosis, they were no longer tied to the vents. ATP Cells left the vents on two separate occasions. ATP Eubacteria This marks the beginning of life. Archaea Own Own energy energy Eukaryota production production Energy gradient Within hydrothermal vents First metabolic pathways, Co-factors Replicators, Enzymes Differential survival Differential survival Homeostasis Homeostasis Reproduction Reproduction Outside hydrothermal vents Differential reproduction rates Growth Differential reproduction rates Growth Standard chemical Problems reactions driven by electrochemical RNA –DNA interplay? gradients Oligonucleotids and Generation of proteins need chiral autonomous monomers. electrochemical Because all bubbles gradients eventually decay Autonomous differential survival does chemical cycles not mean differential proliferation of How long do autonomous cycles. bubbles survive? Full onset of evolutionary process No replicator transfer between bubbles. All has to be within one lucky bubble? The question of time. Full life in common sense If fast evolution to life why only two primordial domains? Or do more exist? Life started at higher temperatures Reconstruction of thermooptima of ancient enzymes Gouy, Chaussidon. 2008. Nature 451: 635 The archaean strain 121 grows at 121° C. 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 Nanobes (10-150 nm) Nanobacteria (50-500 nm) Mycoplasma genitalium (300 nm) smallest known bacterium Pelagibacter ubique (500-600 nm) Mimivirus (400 nm) largest known virus infects Amoeba Escherichia coli (2000-6000 nm) 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. 150º C. 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. Nanobes from Austrian thermal springs Thermal springs represent 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 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 s: a measure of selective superiority (fitness) z Manfred Eigen (1927- Replicator size N s N ln( ) 1 p Region of viable systems p: the mean probability of correct replication of Nmin a nucleotide 1-p is therefore the error rate 1-pmin Error rate per base (1-p) Early replicator systems with high copying error rates had only limited information content The oldest remains of life Stromatolites from the Gunflint Formation, Ontario, Canada 1900 Mya are remains of Cyanobacteria Archaeoscillatoriopsis maxima Marble Bar in Western Australia 3500 Mya. It might be a Cyanobacterium Oldest known sure eucaryotes (chlorophytes) from San Berhardino, California having 1400 Mya. Bacterium from Western Australia, 3500 Mya. Again it might be a Cyanobacterium A major invention: Endosymbiosis Mitochondrion Chloroplasts Lynn Margulis (1938-) Zooxanthellae within hermatypic corals and giant clams Cyanobacteria 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 Percent present O2 level The rise of the oxygen level 100 10 1 0.1 0.01 0.001 0.0001 0.00001 First Eucaryotes First metazoa Cyanobacteria -4 -3 -2 -1 Age [bilions of years] 0 After Anbar (2008) and Frey et al. (2009) Why did oxygen levels increase? 1. Plate tectonic changed the demands of oxygen to react with volcanic lava 2. Cyanobacteria invented photosynthesis 3. Effective photosynthesis of cyanobacteria within first eucaryotes 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. Sexual reproduction is an autapomorphy of all eukaryotes Many eukaryote lineages returned to asexual reproduction Andricus spec. Rotifera In principle sex is disadvantageous because • Asexual populations reproduce faster Sexual Asexual • Recombination destroys advantageous allele combinations • Sexual reproduction needs investment in gamete production and growth Taraxacum spec. Most asexual (parthenogenetic) species are phylogenetically young. Bdelloid Rotifera are an exception and pose a theoretical problem. Why sex? Muller’s ratchet 60 In an asexual species deleterious mutations might increase over time. Occurrences z 50 40 The frequency of individuals without deleterious mutations decreases. 30 20 10 0 0 1 Zero category decreases 2 3 4 5 6 7 8 9 1 2 Time 3 10 11 12 Number of deleterious mutations 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 Why sex? Adaptation to changing environments Sexual species F1 A B C Asexual species F1 A B C Mutation F2 AB AC BC F2 AA BB BC Sex generates additional genetic variability. The adaptational advantage might counterbalance the costs of sex DNA repair during meiosis DNA glycosylase AP endonuclease DNA polymerase 1 DNA ligase Syngamy allows for DNA repair and therefore reduced replication error probabilities. According to the Eigen equation this allows for larger genome size. The basic tree of eukaryotic life Rhodophytes Vascular plants Chlorophytes Glaucophytes Chloroplasts Myxomycetes Chromalveolatae („Diatomea”, „Ciliatae”) Discicristates („Euglenoidea”) 1.6-1.8 mya 1.0-1.6 mya Metazoa 0.8-1.5 gya Choanoflagellates Fungi Cercozoa („Foraminifera”) Excavates („Flagellata”, „Amoeba”) Nucleus Sex Mitochondria Root 2.0-2.7 gya Cavalier-Smith 2002, 2003 Chromalveolata Plantae Chromista Alveolata Endosymbionts The basic tree of eukaryotic life Contains many paraphyletic groups (grades) Plastids Archezoa Discicristata Excavata Metazoa Euglena Porifera Lamblia Choanozoa Eumycota Heliozoa Cercozoa Rhizaria Rhizopoda Heliozoa Saccharomyces Opisthokonta Apusozoa Why are there no early evolutionary stages of eucaryotes? Mycetozoa Bikonta 2 cilia The problem of missing links. Unikonta Ancyromonas 1 cilium,Nucleus, Cytoskeleton, 80 S Ribosomes, Peroxysomes Mitochondrium Lobosa Root (2.0-2.7 Gya) Archamoeba Arcella Slime mold Amoebozoa 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.html http://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