04_EVOW_CH04 06_EVOW_CH04 Origin of life is to large extent outside evolutionary biology ® in essence, it is interdisciplinary study: chemistry (nature of substances composing organisms), geology, study of atmosphere (nature of environment in which life has emerged) etc. Actually, what is life? Pictorial art Zdenek Burian Neanderthal fire & rainbow definitions: phenotypic evolutionary Muller (1966): autoreproduction variability inheritance Barton et al. (2007): autoreproduction and natural selection prerequisite: ability to accumulate substances and their organization in more complex structures prerequisite: memory of the system prerequisite: metabolism What is life? J. Maynard Smith & Eörs Szathmáry (1999): prerequisite: heritable variation Problem of study of the origin of life: J. Monod: evolutionary tinkering, always short-term advantage or coincidence, never long-term perspective ´ assessment of evolution from backward view, with respect to long-term consequences Þ present-day life cannot help with solving criticisms from creationists: nobody has succeeded to create life in the tube Výsledek obrázku pro russian diy cars Výsledek obrázku pro russian diy cars skenovat0007 Evolution in the tube: Sol Spiegelman et al. (1970): RNA (template ~ 4500 bp) and bacteriophage Qb replicase, + nucleotides (normal size jpg) Sol Spiegelman skenovat0003 Þ evolution ® „Spiegelman´s monster“: ® reduction of size after 74th transfer to 218 bp » 5% size of the original RNA*) Þ increase of replication rate ® decrease of the ability to infect E. coli after 4th transfer reduction of infectiousness But these experiments don´t explain origin of life (enzyme supplied) Sumper a Luce (1975): origin of the „Spiegelman´s monster“ even without template (only RNA bases and Qb replicase) *) Oehlenschläger a Eigen (1997): finally only 48-54 bp (~ binding site for RNA replicase) lower limit: oldest rocks gneiss in Great Slave Lake (Canada) – 4 GY zircon crystals (Australia) – 4,3 GY some meteorites – 4,5 GY end of bombarding of Earth – ~4 GY upper limit: microfossils, chemical fossils chert in Warrawoona Group (Z Australia) 3,45 GY: resemblance to present stromatolites ... now questioned ORIGIN OF LIFE According to radiometric measurements age of Earth ~ 4,54 ± 0,04 GYA (but according to some theories Earth has been created secondarilly and so it is younger) present-day stromatolites Shark Bay, W Australia Precambrian stromatolites Siyeh Formation, Glacier Natl. Park chemical fossils – kerogen = organic matter created by decay and transformation of living organisms Greenland glacier: 3,85 GY, confirmed by C12/C13 ratio Conclusion: life has probably emerged during 200 MY between 4 and 3,8 GY https://whyevolutionistrue.files.wordpress.com/2010/02/microfossils.jpg?w=1000 nucleus? Emmanuelle Javaux et al. (2010): „acritarchs“ - 3,2 GYA (Agnes gold mine, Moodies Group, S Africa) before – 1,8 GYA není jisté, zda jde o eukaryota cell wall more complex cell structures 1,4 GYA How has life arisen? origin of simple organic molecules ® chemical evolution, primitive metabolism origin of autoreplication, compartmentation and origin of cells, ... First chemical experiments: 1828: ammonium chloride + silver cyanate + heat ® urine (= Wöhler synthesis) 1850s: formamide + H2O + UV, electricity® alanine formaldehyde + NaOH ® saccharides Þ evidence against vitalism (claims that chemistry in living systems is fundamentally different from non-living, ie. organic ¹ inorganic) Alexandr Ivanovich Oparin (1924) J. B. S. Haldane (1928) reducing atmosphere: hydrogen, water, methane, ammonia Stanley L. Miller, Harold C. Urey (1953): methane + ammonia + H2 + H2O ® 10-15 % carbon in organic compounds 2 % carbon ® amino acids, lipids, carbohydrates building components of nucleic acids A.I. Oparin J.B.S. Haldane H.C. Urey S.L. Miller Chemical evolution 06_EVOW_CH04 „oceanic“ part: water evaporates by heating; H2, CH2 and NH3 added „atmospheric“ part: spark discharges simulate lightnings and supply energy cooling and condensation of gases in the „ocean“ organic compounds emerge Problems: according to current knowledge the atmosphere then less reducing: CO2, N2, H2O and others Þ consequently much less molecules arising not all nucleotides synthesized phosphorus in nature rare some compounds in minimal amounts some products highly unstable (eg. along with ribose also other carbohydrates inhibiting ribose synthesis are produced) limited production of long polymers origin of both D and L AA and NA stereoisomers spontaneous origin of ramose, not linear, lipids 18_EVOW_CH04 Where has life originated? Darwin: „hot little pond“, prebiotic soup alternatives: extraterrestric origin: panspermia: Svante August Arrhenius existence of organic compounds in universe (comets, meteorites): eg. Murchison meteorite (1969, Australia): 4,6 GYA; many compounds as in the Miller-Urey experiment bubbles: clouds, sea spume Thomas Gold (1970): life deep under beneath the surface – existence of extremophilic archaebacteria up to 5 km beneath surface S. A. Arrhenius hydrotermal vents = “black smokers“ Günter Wächtershäuser thermal energy rather than Sun chemical synthesis: carbon fixation by chemical energy protection against UV radiation and meteorite impacts fixation of unstable molecules by cold water around the vents 1977: thermophilic bacteria and archaebacteria, three-meter tube worms, bivalves, starfish, barnacles, limpets, crabs, annelids, shrimps Khun2 G. Wächtershäuser G. Wächtershäuser: life on the pyrite surface = the Fe-S world hypothesis „prebiotic pizza“ on the pyrite surface molecule clusters [2Fe-2S] or [4Fe-4S] ® potential precursors of ferredoxins, pyridoxalphosphates, folates, and cofactors (NAD) central role of acetyl-CoA chemoautotrophy Advantages of flat surface: thermodynamics: lower entropy kinetics: higher probability of molecule colisions supply of ions to reactions (not clay!) production of linear lipids easier removing of water molecules Origin of replicators – RNA world Experiments of Spiegelman, Sumper and others have shown that on the replicátor level there is not only heredity and mutation but also selection but WHAT was replicated? proteins DNA RNA something else proteins DNA RNA something else F. Crick C. Woese L. Orgel Francis Crick, Carl Woese, Leslie Orgel (1967): dual role of RNA: heredity + enzyme = ribozyme Origin of replicators – RNA world Experiments of Spiegelman, Sumper and others have shown that on the replicátor level there is not only heredity and mutation but also selection but WHAT was replicated? RNA characteristics: simpler than DNA absence of complex repair mechanisms ability to build multiple 3D conformations more reactive than DNA (OH-group on 2´ carbon) http://2.bp.blogspot.com/-fTqQnoy_3DE/TdfsOqm10fI/AAAAAAAADE0/p1u0Yr_yCT4/s1600/DNArepair.gif http://www.evolution-textbook.org/content/free/tables/Ch_04/T3_EVOW_Ch04.jpg http://www.evolution-textbook.org/content/free/figures/04_EVOW_Art/15_EVOW_CH04.jpg http://www.evolution-textbook.org/content/free/figures/04_EVOW_Art/15_EVOW_CH04.jpg many functions have arisen long ago RNA as „molecular fossils“ many essential coenzymes, eg. NAD+, flavin adenin dinucleotide (FAD) = ribonucleotide derivates deoxyribonucleotides arise from ribonucleotides RNA primer is used during DNA replication ATP = ribonucleotide Kruger et al. (1982): self-cleaving of intron in pre-mRNA of Tetrahymena File:Tetrahymena thermophila.png Kruger et al. (1982): self-cleaving of intron in pre-mRNA of Tetrahymena Zaug a Cech (1986): IVS (intervening sequence) ® ribozyme ribozyme active site ligase activity polymerase activity File:Tetrahymena thermophila.png Doudna a Szostak (1989): modification of IVS ® catalysis of synthesis of complementary strand according to external template – max. 40 nucleotides, only 1% complete Doudna (1991): three-subunit ribozyme from sequence of sunY of T4 bacteriophage ability to replicate also other RNAs compartmentation necessary Paul & Joyce (2002): R3C ribozyme – ligation of two RNA molecules R3C modified so that the ligation product is identical to R3C ® catalysis of own replication ´ only two rounds of replication and absence of selection (no variation) ® these problems later solved (Lincoln & Jozce 2009) Some known natural ribozymes: peptidyl transferase 23S rRNARNase P introns of groups I and II hairpin ribozyme GIR branching ribozyme leadzyme hammerhead ribozyme HDV ribozyme mammal CPEB3 ribozyme VS ribozyme glmS ribozyme CoTC ribozyme http://www.evolution-textbook.org/content/free/tables/Ch_04/T4_EVOW_Ch04.jpg Alternatives to nucleic acids: Alexander Graham Cairns-Smith: crystalic clay as „urgene“ – initially anorganic replication, a kind of „scaffold“ Julius Rebek: autoreplication using AATE (amino adenosin triacid esther) Ronald Breaker (2004): DNA can bahave as ribozymes cairnssmith_ph A.G. Cairns-Smith File:Rebek.jpg J. Rebek Problem of ribozyme-aided replication: Manfred Eigen (1971): individual genes will compete without repair mechanisms maximum size of replicating molecules » 100 bp length of DNA segment encoding functional enzyme much exceeds 100 bp = Eigen paradox hypercycles = stable coexistence of two or more cooperating replicators hypercycles: molecular mutualism: reciprocal altruism (win-win relationship) competition of the whole systém with other cycles risk of systém „parasitation“ Þ need for compartmentation http://images.slideplayer.com/32/9816579/slides/slide_23.jpg role of tiny crevices and unevenness of the mineral surface Compartmentation and origin of cells felspar clay layers protection, increase of concentration role of tiny crevices and unevenness of the mineral surface proteins: microspheres (Sidney W. Fox) lipids: spontaneous production of liposomes spontaneous production of lipidic membranes: „oil on water“ ® „water on oil“ semi-cell ® proto-cell ® cell http://www.evolution-textbook.org/content/free/figures/04_EVOW_Art/14_EVOW_CH04.jpg Compartmentation and origin of cells fusion of replicators Þ longer replication Þ selective disadvantage possible benefits: 1. reduction of competition between functionally connected replicators 2. products of functionally connected replicators at the same place genetic code: redundant, redundancy random (Ser, Arg, Leu: 6 codons ´ Met, Trp: 1 codon) Origin of chromosomes and genetic code anticodon mycop chemically related AAs ® similar code genetic code is not by far „universal“ – exceptions in some organisms (eg. Mycoplasma) or organelles (mitochondria) AAs perhaps initially helped to stabilize RNAs or as enzymatic co-factors enhancing RNA activity ® step by step emergence of function in translation system P site A site emerging protein mRNA tRNA ribosome bond of AA Association AAs and RNAs: synthesis of proteins governed by RNA mapping of RNA sequence onto AA origin of tRNA „frozen accident“ – F. Crick (1968) some RNA molecules evolved ability to transfer AA to other RNA selection gradually favours one or more RNAs for each AA association between AA and RNA random stereochemical theory: Carl Woese different RNAs tend to preferentially bind particular AAs ® some experiments show that RNA molecules may be selected according to their preferential bond to particular AAs RNA world: RNA = both genotype and phenotype with translation proteins adopt most catalytic RNA functions (they can create broader range of polymers) Þ much more diverse catalytic activities ® eg. no RNA molecule can catalyze redox reactions or break C–C bonds DNA advantages: lower reactivity Þ higher stability Þ longer genes division of labour between RNA and DNA with loss of genetic function RNA could have carry out catalytic and structural functions with smaller restrictions Transition RNA ® DNA 2 2 Origin of eukaryotic cell 2 http://casopis.vesmir.cz/files/image/id/22576 Thomas Cavalier-Smith: loss of cell wall Þ necessity to create endoskeleton Þ flexibility, movement, fagocytosis invagination of membrane ® ER File:Thomas Cavalier-Smith.jpg Prokaryotic cytoskeleton: FtsZ: tubuline analogue, function in cell division MreB: actin analogue, rod-shaped cell shape Crescentin: analogue of intermediary microfilaments, helix creation MinD, ParA: no analogue, cell division, separation of plasmids microtubules microfilaments exaptation Origin of cell organelles: Konstantin Sergeyevich Merezhkovsky (1905, 1909): term symbiogenesis chloroplasts = originally alien organisms (Andreas Schimper, 1883: similarity between chloroplasts and cyanobacteria; Richard Altmann, 1890: mitochondria [bioblasts] = originally bacteria) first animal cell: anucleate amoeba + bacterium (nucleus) Lynn Margulis (1966, 1970): endosymbiosis mitochondria: bacteria related to rickettsias or other a-proteobacteria (eg. Rhodospirillum), gradually loss of photosynthesis chloroplasts: cyanobacteria, loss of respiration File:Merezhkovsky K S.jpg K.S. Merežkovskij [USEMAP] Lynn Margulisová nucleus mitochondrion primary plastid Theories of the origin of nuclear membrane: 1. fusion of vesicles of cytoplasmatic membrane 2. fusion of eubacterium and archaebacterium (archaebacterial membrane = nuclear, bacterial membrane = cellular) 3. viral origin (several alternatives) ... controversial 4. first origin of the 2nd cytoplasmatic membrane, from the inner eventually nuclear membrane http://www.evolution-textbook.org/content/free/tables/Ch_08/T2_EVOW_Ch08.jpg Transfer of genes to nucleus: eg. neoSTLS2 gene, tobacco chloroplast ® in 16 of 250 000 (» 1/16 000) daughter cells transfer of the gene to nucleus Þ kanamycin resistence peroxisomes: G+ bacteria microtubules: spirochaetes ´ současné poznatky nepotvrzují Mixotricha paradoxa spirochaetes secondary and tertiary endosymbiosis ® complex plastids: eg. euglena + green alga http://www.dr-ralf-wagner.de/Bilder/Euglena_gracilis.jpg http://upload.wikimedia.org/wikipedia/commons/e/ea/Euglena_diagram.jpg Secondary endosymbiosis: loss of cellular content of primary host https://classconnection.s3.amazonaws.com/114/flashcards/717114/png/picture_101318883077918.png Secondary endosymbiosis: http://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/14256762/endosymbiosis_Figure1_2 _1.jpg http://www.life.umd.edu/labs/delwiche/pubs/endosymbiosis.gif Tertiary endosymbiosis: sometimes the existence of a secondary endosymbiont can be revealed only according to presence of its DNA (eg. chlamydia genes in plant plastids and primary algae) in other cases endosymbionts still able of independent life, eg. photosynthetic algae (chlorellas, dinoflagellates, haptophytes) in cells of corals, foraminiferans, radiolarians, and some ciliates http://juicing-for-health.com/wp-content/uploads/2015/04/chlorella-algae.jpg http://1gr.cz/fotky/idnes/08/043/maxi/KOT22b4a1_lili_protoperidinium.jpg http://i.idnes.cz/08/111/maxi/JBA26f2b6_112814_1354415.jpg https://upload.wikimedia.org/wikipedia/commons/thumb/b/b0/Gephyrocapsa_oceanica_color.jpg/230px-Gep hyrocapsa_oceanica_color.jpg Chlorella haptophyte Gephyrocapsa Ceratium Protoperidinium Elysia viridis http://www.conchsoc.org/sites/default/files/Ian%20Smith/3Ev.jpg http://img.news.sina.com/technology/p/2011/1128/U48P5029T2D418111F24DT20111128173116.jpg dinophysis_caudata.jpg http://www.eos.ubc.ca/research/phytoplankton/ciliates/myrionecta/images/small/M_rubra_fixed_20xDIC_ ann.jpg Myrionecta rubra Dinophysis caudata „kleptoplastids“ (eg. ciliate Myrionecta rubra, dinoflagellate of the genus Dinophysis, marine gasteropod Elysia viridis) Origin of multicellular organisms http://upload.wikimedia.org/wikipedia/commons/4/4b/Dictyostelium_Aggregation.JPG http://i.telegraph.co.uk/multimedia/archive/01807/amoeba_1807435i.jpg sorus stalk 20-22 h 24 h fruiting body 16 h „finger“ 18 h „Mexican hat“ „slug“ 12 h tight aggregate 10 h loose aggregate 8000–500 000 cells slime molds, eg. Dictyostelium discoideum http://cronodon.com/images/Dictyostelium_Grex.jpg How can „slug“, composed of independent amoebas, orient itself in its environment? cAMP (cyclic adenosine monophosphate): emission in area of the densest aggregation ® signal for „downstream“ cells ® gradual aggregation production of protein enabling mutual attachment of amoebas reaction to external stimuli: light, teperature, oxygen and ammonium in the soil http://upload.wikimedia.org/wikipedia/commons/4/4b/Dictyostelium_Aggregation.JPG cAMP emission http://www.corbisimages.com/images/Corbis-42-26608347.jpg?size=67&uid=16a1b7b1-53c8-4d0c-9a4b-dca31 bb1e1bb Advantages of D. discoideum aggregation? production of coat made of cellulose and substances rich of proteins ® protection against nematodes – only on the “slug“ surface faster movement nematode „slug“ protected by coat and size direction of „slug“movement http://www.evolution-textbook.org/content/free/figures/05_EVOW_Art/11_EVOW_CH05.jpg Last Universal Common Ancestor (LUCA) we can know nothing about organisms before LUCA Tree of life: http://evolution-textbook.org/content/free/figures/00END_EVOW_Art/02_EVOW_END.jpg http://www.evolution-textbook.org/content/free/figures/05_EVOW_Art/17_EVOW_CH05.jpg ? ? ? a b Eubacteria (E. coli) mitochondria (cows) chloroplasts (tobacco) Archaea (Sulfolobus) Eukaryotes (plants, fungi) Eubacteria (E. coli) chloroplasts (tobacco) Archaea (Sulfolobus) Eukaryotes (plants, fungi) ATPase Horizontal transfer of genes http://www.evolution-textbook.org/content/free/figures/05_EVOW_Art/23_EVOW_CH05.jpg reticulate evolution Þ no LUCA of recent organisms ´ trees for individual genes can have LUCA Where to place viruses on the Tree of Life? 1. relics of pre-cellular world: some processes and genes ancient many genes only very distantly related to their cellular counterparts ´ how could they independently exist in pre-cellular world? 2. similarity with transposons ® „escaped“ parts of cellular organisms – (eg. RNA or DNA elements, plasmids) 3. originally free-living organisms eg. mimivirus: genome size = 1,2 Mb, > 900 proteins, ie. more than some bacteria and archaebacteria! mimivirus Increase of complexity: Stephen Jay Gould: evolution moves as a drunk person which cannot return to the starting point however he wants even at present most organisms prokaryotic secondary simplification (eg. parasites) ´ John Maynard Smith a Eörs Szathmáry: the contingent irreversibility theory): steady tendency to increase of complexity major transitions complexity emrges withou selection alt14 http://www.achievement.org/achievers/gou0/large/gou0-006.jpg http://eu-media1.webofstories.com/images/1004/1004.jpg http://www.oxfordlearnersdictionaries.com/media/american_english/fullsize/r/rat/ratch/ratchet.jpg Major transitions in evolution: origin of replicators compartmentation, origin of cell origin of chromosomes origin of genetic code, DNA origin of Eukaryotes origin of sex multicellularity societies origin of language Individuals cease to reproduce independently Bigger size ® bigger pray, specialization, division of labour Origin of more effective ways of acquiring, processing, transmission, and saving of informations http://ecx.images-amazon.com/images/I/81O%2Ba60qQbL.jpg conflict of selections at different levels: replication control ´ B chromosomes, transposition fair meiosis ´ meiotic drive differentiation of somatic cells ´ oncogenic growth non-reproducing castes ´ egg-laying workers But advantages of a transition to a „higher level“ do not imply group selection!