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: alar@ciencias.unam.mx

Weizmann Institute 2013

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

The heterotrophic theory of the origin of life:

a contemporary reassessment

DNA/RNA/protein cells

RNA World

synthesis & accumulation of organic compounds

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)

The gene complement of the last common ancestor (cenancestor, LCA, LUCA)

Delaye, Becerra & Lazcano (2005) Origins Life Evol Biosph 35: 537

Highly conserved protein domains

(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

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.

Unknown prebiotic chemical processes?

Evolutionary outcome of pre-RNA worlds?

RNA World

The Miller experiment (1953)

Miller, 1953

Preliminary analyses of S.L. Miller 1953 samples

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

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:

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)

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

Organic compounds in the 109 years-old Murchison meteorite

Deamer 2011

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

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)

Burton et al 2013

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.

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 

Synthesis of monomers under possible prebiotic conditions produce appreciable yields under a wide range of environmental settings*

Miller & Lazcano, 2002

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)

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

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

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?

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

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

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

Burton et al 2013

Genetically-encoded amino acids

Cleaves 2010

Genetically-encoded amino acids

Cleaves 2010

Amino acids are abundant in chondritic meteorites and are readily formed in model prebiotic reactions.

This is not true of:

a) arginine & lysineb) histidine

Histidine

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?

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

Harold White’s hypothesis: is histidine an evolutionary remmant of a catalytic ribonucleotide?

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….

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.