Transcript Planetary evolution and biochemical adaptations

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 Lazcano
Facultad de Ciencias, UNAM
MEXICO
E-mail: [email protected]
Weizmann Institute 2013
Our understanding of the origin of life is
strongly hindered by
1. lack of geological evidence of the prebiotic
environment
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
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)
Adapted from Futuyma (2006) Evolutionary Biology (Sinauer, Boston)
The gene complement of the last common
ancestor (cenancestor, LCA, LUCA)
Highly conserved protein domains
Delaye, Becerra & Lazcano (2005) Origins Life Evol Biosph 35: 537
RNA: no more a mere molecular go-between
large nc RNA
(rRNA, tRNA, primer RNA)
small nc RNA
(Argonaute/Piwi RNA)
non-coding RNA
(nc RNA)
coding RNA
(c RNA)
RNA
deoxyribonucleotides
ribonucleotides
ribose-P, amino acids, CO2, NH3
coenzymes
histidine
alarmones
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.
RNA World
Unknown prebiotic
chemical processes?
Evolutionary outcome of
pre-RNA worlds?
The Miller experiment (1953)
Miller, 1953
Preliminary analyses of S.L. Miller 1953 samples
Note: identifications
were confirmed by
LC-FD/ToF-MS
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; 9D,L--ABA; 10--AIB; 11-D,L--ABA; 12-D,L-Isovaline; 13-D,L-Norleucine. (* are unidentified
peaks); and (E) a procedural blank.
The evidence suggests that prior to the origin
of life the primitive Earth already had:
 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
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)
The prebiotic broth: a useful metaphor cooked with a
wide range of ingredients
CO2, CO, N2, H2S, H2O, CH4
amino acids, nucleobases, sugars, lipids,
oligomers of biochemical compounds
CO2, NH3, H2S, H2O
Lazcano, Natural History (Feb/2006)
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
Blue, meteoritic aa; red, Miller’s volcanic experiment (CH4, H2O, NH3,H2,);
black, spark discharge simulation (CH4, CO2, H2O, NH3, H2, H2S)
Parker et al. (2011) PNAS 108: 5526
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
CH3
O
O
H3C
OH
NH2
S
OH
H3C
Valine (Val)
NH2
Methionine (Met)
O
O
H3C
OH
H3C
CH3
NH2
NH2
Leucine (Leu)
Norvaline (Nva)
O
H3C
OH
CH3
OH
H3C NH2
Isovaline (Iva)
O
H3C
OH
NH2
Isoleucine (Ile)
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
Both norvaline (Nva) and norleucine (Nle) are incorporated
in vivo in recombinant hemoglobin in E.coli
Apostol et al. (1997) J. Biol. Chem. 272: 28980
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)
Figure 6-59a Molecular Biology of the Cell (© Garland Science 2008)
2. Which is the intracellular source of non-protein aliphatic
amino acids like norvaline and norleucine?
Biosyntheses of protein & non-protein aliphatic amino acids
pyruvate
isoleucine
threonine
-ketoisovalerate
valine
-ketobutyrate
-ketoisocaproate
leucine
-ketovalerate
norvaline
-ketocaproate
norleucine
Bogosian et al. (1989) J. Biol. Chem. 264: 531
Biosyntheses of protein & non-protein aliphatic amino acids
pyruvate
isoleucine
threonine
-ketoisovalerate
valine
-ketobutyrate
-ketoisocaproate
leucine
-ketovalerate
norvaline
-ketocaproate
norleucine
Bogosian et al. (1989) J. Biol. Chem. 264: 531
Under anaerobic conditions, pyruvate production is
quickly enhanced –followed by a significant
increment of intracellular norvaline
Soini et al. (2008) Microbial Cell Factories 7: 30
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 & lysine
b) 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?
Propensity of a residue to be catalytic in each of the six classes of enzymes
EC 1, oxidoreductases
EC 2, transferases
Holliday et al (2011) FEBS J 278: 3835
EC 3, hydrolases
EC 4, lyases
EC 5, isomerases
EC 6, ligases
Harold White’s hypothesis: is histidine an evolutionary
remmant of a catalytic ribonucleotide?
CONCLUSIONS….
synthetic efficiency, physical stability, chemical
reactivity, self-assembly, self-organization
prebiotic
synthese
s
lipids
noncanonical bases
imidazolides
racemic sugars
racemic nonprotein &
(some) protein amino
acids
natural selection
catalytic RNA
amino acids
lipids
cells with RNA,
proteins & DNA
time
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.