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Transcript of 27º Meeting of the Israel Society for Astrobiology and the Study of the Origins of Life Planetary...
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27º Meeting of the Israel Society for Astrobiology and the Study of the Origins of Life
Planetary evolution and biochemical adaptations: between contingency and determinism?
Antonio LazcanoFacultad de Ciencias, UNAM
MEXICOE-mail: [email protected]
Weizmann Institute 2013
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Our understanding of the origin of life is strongly hindered by
1. lack of geological evidence of the prebioticenvironment
2. absence of a fossil record of prebiological systems 3. lack of an all-embracing generally agreed definition
of life
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The heterotrophic theory of the origin of life:
a contemporary reassessment
DNA/RNA/protein cells
RNA World
synthesis & accumulation of organic compounds
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Adapted from Futuyma (2006) Evolutionary Biology (Sinauer, Boston)
Current limits of molecular phylogenies(DNA/RNA/protein cells)
RNA/protein cellular systems(inferred from metabolic data)
RNA World(deduced from ribozymes)
primitive soup(experimental simulations & extraterrestrial organic molecules)
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The gene complement of the last common ancestor (cenancestor, LCA, LUCA)
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Delaye, Becerra & Lazcano (2005) Origins Life Evol Biosph 35: 537
Highly conserved protein domains
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(rRNA, tRNA, primer RNA)
ribonucleotides
coenzymes
histidine
alarmones
RNA
coding RNA(c RNA)
non-coding RNA(nc RNA)
deoxyribonucleotides
ribose-P, amino acids, CO2, NH3
large nc RNA small nc RNA(Argonaute/Piwi RNA)
RNA: no more a mere molecular go-between
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The limits of molecular phylogenies
At the time being, molecular phylogenies cannot be extrapolated to an evolutionary period prior to the emergence of ribosome-mediated protein synthesis.
There is nothing in molecular cladistics that supports the possibility of ancestral life with replicative and metabolic abilities based solely on RNA molecules.
Evidence for the RNA World comes from the catalytic versatility of ribozymes and is supported by the biological ubiquity of RNA and ribonucleotides. For instance, rRNA-mediated peptide bond formation is a strong indication that protein synthesis first evolved in an RNA world.
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Unknown prebiotic chemical processes?
Evolutionary outcome of pre-RNA worlds?
RNA World
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The Miller experiment (1953)
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Miller, 1953
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Preliminary analyses of S.L. Miller 1953 samples
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Representative cumulative HPLC chromatograms for: (A) classic apparatus design; (B) volcanic apparatus design; (C) silent discharge apparatus design; and (D) an amino acid standard; peak identifications 1-D,L-Asp; 2-L,D-Glu; 3-D,L-Ser; 4-Gly; 5--Ala; 6-ABA; 7-D,L--AIB; 8-D,L-Ala; 9-D,L--ABA; 10--AIB; 11-D,L--ABA; 12-D,L-Isovaline; 13-D,L-Norleucine. (* are unidentified
peaks); and (E) a procedural blank.
Note: identificationswere confirmed by
LC-FD/ToF-MS
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a wide array of organic compounds of biochemical significance –and not only proteinic amino acids
many inorganic & organic catalysts
many different purines & pyrimidines (the potential for template-directed polymerizations)
membrane-forming compounds
The evidence suggests that prior to the origin of life the primitive Earth already had:
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Some examples of self-organization which may be
relevant to the origin of life
1. Formation of micelles, liposomes and lipid vesicles from
prebiotic amphiphiles;
2. Self-assembly of nucleic acids (base-bearing polymers);
3. Fe-S catalytic clusters;
4. Mineral and organic compounds complexes (clays and
bases); and
5. Autocatalytic synthetic reactions (formose reaction)
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CO2, CO, N2, H2S, H2O, CH4
CO2, NH3, H2S, H2O
amino acids, nucleobases, sugars, lipids, oligomers of biochemical compounds
Lazcano, Natural History (Feb/2006)
The prebiotic broth: a useful metaphor cooked with a wide range of ingredients
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Organic compounds in the 109 years-old Murchison meteorite
Deamer 2011
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Relative abundances of amino acids in the Murchison meteorite and their synthesis in a CH4, NH3, & H2O primordial atmosphere
Parker, Cleaves, Dworkin, Glavin, Cahallan, Aubrey, Lazcano & Bada, 2011
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Parker et al. (2011) PNAS 108: 5526
Blue, meteoritic aa; red, Miller’s volcanic experiment (CH4, H2O, NH3,H2,); black, spark discharge simulation (CH4, CO2, H2O, NH3, H2, H2S)
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Burton et al 2013
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Moles (relative to glycine = 1) of the various amino acids detected in the volcanic apparatus vials. Amino acids underlined have not
been previously reported in spark discharge experiments.
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Relative aa abundances (gly = 1) for the linear α-aa detected in the target ice sample no. 1 (grey) and target ice sample no. 2 (white)
Martins et al, 2013. Nature Geoscience
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Synthesis of monomers under possible prebiotic conditions produce appreciable yields under a wide range of environmental settings*
Miller & Lazcano, 2002
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H3C
CH3 NH2
OH
O
Leucine (Leu)
H3C
NH2
OH
O
Norvaline (Nva)
H3C
CH3
NH2
OH
O
Valine (Val)
H3CNH2
OH
O
Methionine (Met)
S
H3C
CH3
NH2
OH
O
Isoleucine (Ile)
H3CH3C NH2
OH
O
Isovaline (Iva)
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Why do modern organisms use a small subset of the L -amino acids which are
structurally possible?
“The absence of -amino-n-butyric acid, norvaline and norleucine is most striking and a major challenge to any attempt to account for the selection of the twenty protein amino acids. Their abundance in prebiotic experiments and carbonaceous chondrites is comparable to or greater than the hydrophobic amino acids used in proteins”.
Weber & Miller (1981) Jour. Mol. Evol. 17: 273
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Apostol et al. (1997) J. Biol. Chem. 272: 28980
Both norvaline (Nva) and norleucine (Nle) are incorporated in vivo in recombinant hemoglobin in E.coli
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Figure 6-59a Molecular Biology of the Cell (© Garland Science 2008)
Why are norvaline (Nva) & norleucine (Nle) incorporated into recombinant hemoglobin?
1. Leucyl-tRNA synthase is unable to discriminate between leucine and other aliphatic amino acids (Apostol et al., 1997)
2. Which is the intracellular source of non-protein aliphatic amino acids like norvaline and norleucine?
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threonine -ketoisovalerate valine
isoleucine -ketobutyrate -ketoisocaproate leucine
-ketovalerate norvaline
-ketocaproate norleucine
pyruvate
Bogosian et al. (1989) J. Biol. Chem. 264: 531
Biosyntheses of protein & non-protein aliphatic amino acids
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threonine -ketoisovalerate valine
isoleucine -ketobutyrate -ketoisocaproate leucine
-ketovalerate norvaline
-ketocaproate norleucine
pyruvate
Bogosian et al. (1989) J. Biol. Chem. 264: 531
Biosyntheses of protein & non-protein aliphatic amino acids
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Soini et al. (2008) Microbial Cell Factories 7: 30
Under anaerobic conditions, pyruvate production is quickly enhanced –followed by a significant increment of intracellular norvaline
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Burton et al 2013
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Genetically-encoded amino acids
Cleaves 2010
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Genetically-encoded amino acids
Cleaves 2010
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Amino acids are abundant in chondritic meteorites and are readily formed in model prebiotic reactions.
This is not true of:
a) arginine & lysineb) histidine
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Histidine
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How proteins first evolved is not known, but their active sites must be one of the oldest portions of enzymes.
What do they tell us about their catalytic components?
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EC 1, oxidoreductases EC 3, hydrolases EC 5, isomerasesEC 2, transferases EC 4, lyases EC 6, ligases
Holliday et al (2011) FEBS J 278: 3835
Propensity of a residue to be catalytic in each of the six classes of enzymes
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Harold White’s hypothesis: is histidine an evolutionary remmant of a catalytic ribonucleotide?
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prebiotic syntheses
lipidsnoncanonical basesimidazolidesracemic sugarsracemic nonprotein & (some) protein amino acids
catalytic RNA amino acids
lipids
cells with RNA,proteins & DNA
time
synthetic efficiency, physical stability, chemical natural selectionreactivity, self-assembly, self-organization
CONCLUSIONS….
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Conclusions
1. There is very good evidence for a primitive soup, but the transition from it to an RNA World remains an open question;
2. Experimental simulations of prebiotic environments, analysis of meteorites and stability arguments suggest that RNA was preceded by a complex mixture of genetic polymers with different backbones and nucleobases;
3. The presence of twenty protein amino acids in extant biology does not means that they were essential for the origin of life nor that all of them were synthesized prebiotically; and
4. The key role of imidazolides in prebiotic chemistry and in biological catalysis suggests a connection between the chemical constituents of the RNA World and the emergence of the first proteins.