Cell evolution RNDr. Jan Škoda, Ph.D. Department of Experimental Biology Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Outline - From simple compounds to the world of RNA, DNA and protei - RNA world - From primordial soup to the first cells - From prokaryotes to eukaryotes - Synthetic biology 2 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Cell evolution by natural selection Last universal cellular ancestor (LUCA) - Unicellular organism that is ancestral to all current cellular forms of life - Natural selection requirements: genetic variability, selection of genotypes underlying the highest fitness (reproductive success) domains that include alf rWn the most recent common ancestor of all living things v;? * forebear lineages from before the most recent common ancestor 4 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) From simple compounds to the world of RNA, DNA and proteins 5 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) fl Origin of first complex organic compounds Alexander Ivanovich Oparin (1894-1980) - Russian biochemist (Moscow State University) -Theory of the origin of life (1922, in Russian): - Strongly reducing atmosphere on early Earth (methane, ammonia, hydrogen and water vapor) ■ Simple carbon compounds and inorganic molecules could react to form "building blocks" - nucleotides, amino acids - Gradual chemical evolution from the primordial soup: accumulation of these "building blocks" in the water facilitated their further reactions into polymers (with energy of lightning or sun) and their assembly into units/structures capable of self-replication 6 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Origin of first complex organic compounds John Burdon Sanderson Haldane (1892-1964) - British biologist and mathematician - Proposed a similar theory: The origin of life (1929, in English) - Oparin's work published in English in 1936 Oparin-Haldane hypothesis -Cells self-organized from a primordial soup 7 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Miller (Miller-Urey) experiment -1953: first experimental evidence of possible origin of life from non-living matter -Stanley Miller and Harold Urey A Production of Amino Acids Under Possible Primitive Earth Conditions Stanley L. Miller1' * G. H. Jones Cbemicml Laboratory, Vnivtrtity of Chicago, Chicago, Illinois The idea that the organic compounds that serve as the basis of life were formed when the earth had an atmosphere of methane, ammonia, water, and hydrogen instead of carbon dioxide, nitrogen, oxygen, and water was suggested by Uparin (1) and has been given emphasis recently by Urey {2) and Berne] (.?). In order to test this hypnthesis, an apparatus was bnilt to circulate CH4, NH3, HsO, and H, past an electric discharge. The resulting mixture has been tested for amino acids by paper chromatography. Electrical discharge was used to form free radicals instead of ultraviolet light, because quartz absorbs wavelengths short enough to cause photo-dissociation of the gases. Electrical discharge may have played a significant role in the formation of compounds in the primitive atmosphere. The apparatus used is shown in Fig. 1. Water is boiled in the flask, mixes with the gases in the 5-) flask, circulates past the electrodes, condenses and empties bflek into the boiling flask. The U-tube prevents circulation in the opposite direction. The acids l XAtional Science I-ViihilfittoD Fellow. 1952-53 * Thanks are hi- Ilnrnlil C. Urey for many helpful suxgex-rfons ninl eiititnm-e in the Go MBA nf tills investigation, 528 During the run the water in the flask became noticeably pink after the first day, and by the end of the week the solution was deep red and turbid. Most of the turbidity was due to colloidal silica from the glass. The red color is due to organic compounds adsorbed on the silica. Also present are yellow organic compounds, of which only a small fraction can be extracted wilh ether, and which form a continuous streak tapering off at the bottom on a one-dimensional chro-matogram run in tmtaiml-acetic acid. These snbsliinccs are being investigated further. At the end of the run the solution in the boiling flask was removed and 1 ml of saturated IIgCla was added to prevent the growth of living organisms. The ampholytes were separated from the rest of the constituents by adding Ba(OII)s and evaporating in rm;no to remove amines, adding IT;S04 and evaporat- SCTEWCE, Vol. 117 9 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Miller experiment -Simulated the conditions thought at the time to be present on the early Earth - Mixture of gases: methane, ammonia, hydrogen and water vapor - Electrical sparks (lightnings) -Water condensation and analysis of the solution 11 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Results of Miller experiment - Hydrogen cyanide, formaldehyde - Formic, lactic, acetic, uric acids -Amino acids - 5 reported initially - 23 when the original samples re-analyzed in 2008 - Many following variants: purines and pyrimidines, sugars 12 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Par,* number In IMh'i notebook MWer checked tor the cone experiments, mostly ansno acel*. 11957 l p»rs«o>Uta In this «■ ■ i>« t -if * ii rosrs iron hydroxide, since tome scientists suspected the early earth earned a tot of reOWed iron, John son says. VS. Extraterrestrial organic compounds - Organic compounds are common in space - Purines and pyrimidines found in meteorites 13 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Formation of polymers from organic monomers - Heating of the organic monomers -Catalytic activity of highly concentrated inorganic polyphosphates and other compounds: polyanionic scaffold to assemble macromolecules -Selection for autocatalytic activity, self-replication o-p- -o 0 0-P-- -0 0 O-P-0 o o- <§> 14 BM 700en Cell Biology /11 - Cell evolution (18 May 2022) [1 Polynucleotides - templates for self-replication ■ Hydrogen bonds - base pairing Ě}Mč}{ě}{čKč}{č] 0ĚH^{čHč}{č}{č] E ® A] EH«»] ORIGINAL SEQUENCE FORMS COMPLEMENTARY SEQUENCE ěhMhíhghM] stftp 2 COMPLEMENTARY SEQUENCE FORMS ORIGINAL SEQUENCE 15 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Nucleic acid or protein? Which came first, the chicken or the 16 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) RNA world 2 key features of RNA from the evolution perspective: Encodes information (sequence of nucleotides) Exert different functions (tertiary structure) including catalysis r 17 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Discovery of ribozymes Ribonucleic acid enzymes -RNAs with catalytic functions 1989 Nobel Prize in Chemistry Mendel Genetics Conference A mbutr 10 r.rfjiw [Dtunn Mrndrl im Iii» bicralriuiu JULY 202E Keynote speakers of the conference Cfc 4. ÍI Mendel Genetics Conference 21 July 2022, Brno Thomas R. Cech Interesting interview about breaking the paradigm 18 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Examples of ribozymes Self-splicing introns Peptidyl transferase activity of rRNA in ribosomes P9.1a |t P9.11 Group I intron Ribozyme A«si Pepliden »' R 'tRNAH O (P-site) (FtNft \ (A-3ite| Peptide--'P^A^o IRNA I RNA ACCUGGUACC P2 AGUCUU UAAACCAAUAG P2.1 19 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) (A) replication catalysis S catalytic RNA molecule that ioins together nucleotides to reproduce its own nucleotide sequence and therefore its shape (81 family of mutually supportive catalytic RNA molecules, one catalynng the reproduction of tho others coding RNA (template for protein synthesis) VW\AAsw..... adaptor RNAs new catalytic RNAs ovolve. some of which bind activated amino acids to themselves. By base-pairing to a coding RNA molecule, these RNA molecules allow an RNA sequence to act as a template for the synthesis of amino acid polymors. causing the first genetically determined protein sequences to appear. They thus serve as the first adaptors between nucleotide and amino acid sequences. 3 essential (and hypothetical) steps in transition from RNA to nucleic acid-protein world Ribozyme 1. Self-replication of RNA molecule 2. One RNA molecule catalyzes replication of other molecules 3. Evolution of primitive protein synthesis and genetic code 20 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) RNA-based systems J EVOLUTION OF RNAs THAT CAN DIRECT PROTEIN SYNTHESIS *^RNA and protein-based systems t RNA -n- protein EVOLUTION OF NEW ENZYMES THAT CREATE DNA AND MAKE RNA COPIES FROM IT day cells /^present- Í DNA —RNA protein J nature Explore content v About the journal v Publish with us v Transfer RNA (tRNA) nature > articles > article Article I Open Access | Published: 11 May 2022 A prebiotically plausible scenario of an RNA-peptide world Felix Müller, Luis Escobar, Felix Xu, Ewa Weqrzyn, Milda Nainyte, Tynchtyk Amatov, Chun-Yin Chan, Alexander Pichler & Thomas Carell E Nature 605, 279-284 (2022) | Cite this article 27k Accesses 428 Altmetric Metrics Acceptor stem O CJ D-stem loop O HN^VsTi^NH NO I Anticodon loop [m)nmsU 0 R I H ^ T I R = aa J J Side chain Non-canonical RNA bases (nowdays in tRNA and rRNA) can bind amino acids and establish peptide synthesis directly on RNA Potential origin of ribosome-centered translation 21 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) RNA World 22 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) From primordial soup to the first cells 23 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Coacervates -Small droplets (condensates = dense phase) of biopolymers in a dilute phase (generally water in cells) - Formed through liquid-liquid phase separation - Hendrik G. Bungenberg de Jong ^^^^^^^^^HH Coacervate droplets formed by interaction between gelatin and gum arabic 24 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) fl Coacervation process Optional inserts for the encapsulant Crosslinking 50°C General processing scheme for microcapsule preparation by complex coacervation using gelatin and gum arabic 25 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Membraneless organelles - A. Oparin: life originated as coacervate drops of organic materials -Membraneless organelles: liquid-like compartments arising through liquid-liquid phase separation 26 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Encapsulation - formation of a protocell (b) Exclusive cooperation among nwnbrane-onctOMd molecules. 27 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) 15629914995429449914795599 B RNA chemistry Molecular seHreplication Lipid vesicles appearance Protocell Sett-assembly ot lipids Compositional sell- replication Evolution and internal self-organization Compartment formation and polymerization Two ways of protocell assembly from the primordial soup A. Biopolymer first B. Lipid world 28 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Division by fission o o o ft\p 4) growth O capillary hot í % i) formation of vesicles 2) inclusion of information like DNA/ RNA cold direction of flow vesicle 0 static equilibrium •*-•-—# 50 urn deformation domaining fission static equilibrium 29 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) From prokaryotes to eukaryotes 30 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Evolution reconstruction -Age of fossils - Prokaryotic cells: 3.5 billion years - Eukaryotic cells: 1.5 billion years - Multicellular organisms: 500 million years o o N o z o o s Ui I-O CE O. Geological evidence Oklest mui'ttcclluUir fossils Oldest compartmentalized fossil celts Disappearance of iron from oceans and formation of iron oxides Oldest definite foss»ls Oldest dated rocks Millions of years ago 570 h- 600 - — 1500 — ^-2500 — — 0500 — 4500 Lifo forms Appearance of first multicellular organisms Appearance of first eukaryotos Appearance of aerobic (oxygen-using) respiration Appearance of oxygen-forming photosynthesis (cyanobactoria) Appearance of chemoautotrophs (sulfate respiration) Appearance of Me (prokaryolos): anaerobic (methane-producing) bacteria and anaerobic (hydrogen sulfidc-forming) photosynthesis Formation of the earth Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) 02 levels were almost 50% higher than present First chordates Giant flying insects Invasion of land First photosynthetic bacteria First life First eukaryotes First multicellular eukaryotes First aerobic bacteria First flowering plants A rapid drop of 02 levels occurred at end of the Permian. 02 levels were 25-40% lower than present. 4,000 3,000 2,000 1,000 500 250 100 Present Millions of years ago (mya) 33 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) 34 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) 35 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Evolutionary origin of membrane structures and the cell nucleus nuclear inner nuclear membrane pore complex membrane-bound —5 ribosomes outer nuclear membrane nucleus ancient procaryotic cell ancient eucaryotic cell endoplasmic reticulum cytosol 36 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Origin of mitochondria anaerobic pre-eucaryotic cell nucleus internal membranes early aerobic eucaryotic cell cell membrane aerobic procaryotic cell membrane derived from eucaryotic cell mitochondria with double membrane 37 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Origin of chloroplasts early eucaryotic cell \ photosynthetic bacterium 38 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) early eucaryotic cell capable of photosynthesis chloroplasts with double membrane Endosymbiotic theory -1883 - Andreas W. Schimper ■ Chloroplasts have many similar characteristics to cyanobacteria - Journal footnote: photosynthetic organisms -combination of two separate organisms? -1967/81 - Lynn Margulis: 1967 (Sagan) - „On the origin of mitosing cells" - 1981 - Symbiosis in Cell Evolution - All life is bacterial or derives from bacteria by symbiogenesis 39 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Evidence supporting the endosymbiotic theory Mitochondria & plastids -Surrounded by double membrane - Contain own genome similar to procaryotic: circular DNA, without histones - Replication and division by fission like bacteria -Own protein synthesis apparatus: ribosomes similar to prokaryotic, rRNAs encoded in the own genome Prokaryotic 70S ribosomc Eukaryotic SOS ribosomc 23Sand 5S rRNAs (34 proteins) K.S rKW (21 proteins! 28S, 5.8S, and 5S rRNAs (■»45 proteins) 18S rRNA t-30 proteins) a) E. coli b) Mammalian mitoribosome 40 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Gene transfer to nucleus -Crucial genes retained in the genome of mitochondria or plastids protein import TOM ancestor of mitochondria -5000 genes ancestor of plastids - 5000 genes Further reading plastids 23-200 genes ~2% retained 41 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) 42 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) /C E.coli o 00 6 cyanobacteria Bacillus Sulfolobi Thermotaga' ^ Aquifex Haloferax human Aeropyrum \ Methanothermobacter —Methanococcus yeast —Paramecium —Dictyostelium '--Euglena common ancestor cell 1 change/10 nucleotides ^^^*&jHfinosoma ' Ciardia ' Trichomonas Anaerobic eukaryotes Anaerobic protists - Lack conventional mitochondria: remnants -specific double membrane organelles (e.g., mitosome) - Primitive nature and poorly developed endomembrane system - Parasitic: Giardia, Trichomonas llil Revisited model Endosymbiosis of proteobacterium (mitochondrion) preceded the last eukaryotic common ancestor other bacteria photosynthetic g anjma,s bacteria CyarobacM PHNK Ml » . - , • HKIVB ■ l ■ -i 44 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Mitochondria reduced or even lost during the diversification and evolution of eukaryotes Textbook' Mitochondrion Anaerobic Mitochondrion Mitochondrial genome Oxidative phosphorylation to generate ATP; oxygen is the terminal electron acceptor. Generate ATP but oxygen is not the ternimal electron acceptor; other compounds are used, such as fumarate. Hydrogenosome No oxidative phosphorylation, ATP is generated instead by substrate-level phosphorylation; produce hydrogen. Mitosome Loss of MRO in Monocercomonoides X Most reduced MRO; no electron transport; no oxidative phosphorylation; no ATP generation; participate in Fe-S cluster biosynthesis, localization of the ISC pathway. No more detectable MRO MRO, mitochondria-related organelle 45 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Nuclear envelope Endoplasmic heterotrophic eukaryote Copyright® Pearson Education, Inc., publishing as Benjamin Cummmga. 46 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) The first cells were probably...? 1 What is chemosynthesis? (Bom 47 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) Synthetic biology (18 May 2022) Synthetic biology - Bi9690en Synthetic Biology -Aims to create or redesign new biological systems to achieve specific purposes 2010 - First synthetic genome Science Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Daniel G. Gibson,1 ]ohn I. Glass,1 Carole Lartigue,1 Vladimir N. Noskov,1 Ray-Yuan Chuang,1 Mikkel A. Algire,1 Gwynedd A. Benders/ Michael G. Montague,1 Li Ma,1 Monzia M. Moodie,1 Chuck Merry man,1 Sanjay Vashee,1 Radha Krishna kumar,1 Nacyra Assad-Garcia,1 Cynthia Andrews-Pfannkoch,1 Evgeniya A. Denisova,1 Lei Young,1 Zhi-Qing Qi,1 Thomas H. SegaLL-Shapiro,1 Christopher H. Calvey,1 Prashanth P. Parmar,1 CLyde A. Hutchison III/ Hamilton O. Smith/ J. Craig Venter1-2* We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides ]CVI-synl.O genome starting from digitized genome sequence information and its transplantation into a M. capricohim recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication. 50 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) - Design, synthesis and assembly of bacterial chromosome: Mycoplasma mycoides JCVI-syn01 - DNA segments assembled in yeast -Chromosome introduced into recipient Mycoplasma caprlcolum to replace its genome M 2010 - First synthetic genome Bacteria able to replicate controlled by the synthetic genome - Comprises watermarks (encrypted messages) ■3.5 i S j0419 _' ' i_1 rrra pisx 0420 : phosphate: 0425 t 3426 i0427i 3 ,235 ť239 „240 ^241 rt242 ^243 M244 ^245 „ 246 „247f ,.24£ 0454 11 0455___0460 3 i= j ,278 ť279 ^2B0 ^281 Jim U2BS „289 „290 ^291 292 .29 3 i 0493 i3 i-3495igj 0497 j-3498 S1"^ '" '.-.NA': Bi0504_ 0505 1 V 322 .323 „324 „325 „326 „327 „32B „329 „330 .331 „332 „33 1. Explanation of the coding system itself 2. URL address for those who deciphered the code 3. Names of all authors and co-workers 4. Famous quotes (James Joyce, Richard Feynman) 51 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022) ABCDEFG-BI L M H O P R E T Q V W Y TAG AGT TTT ATT TAA GGC TAG TCA CTĚ GTT GCA AAC CAA TGC CGT AGA TTA CTA GOT TGA TCC TTG GTC GGT CAT TGG - Watermark one: - J. CRAIG VENTER INSTITUTE 2009 ABCDEFGHIJKLMNOPQRSTUVWXYZ 0123456789?@??-??=/:??????"??!'., SYNTHETIC GENOMICS, INC. GENOME TEAMTHE JCVk/AxP>PROVE YOU'VE DECODED THIS WATERMARK BY EMAILING US HERE! 52 Bi1700en Cell Biology /11 - Cell evolution (18 May 2022)