From molecular evolution to

1
From molecular evolution to cellular life Kirsi
Lehto University of Turku
2
Life as we know it... Life before the DNA-protein
world RNA world ... Possible relicts of the RNA
world ... Problems of the RNA world Where could
it exist, or come from....
3
Life,as we know it ...
-all life is cellular -life is (mediated via)
complex biochemistry multiple highly regulated
enzyme reactions in aqeous solution -cellular
biochemistry is regulated by genetic information
4

• DOGMA OF LIFE
• -genetic information is
• encoded in the nucleotide
• sequence of DNA,
• -copied (transcribed) into the
• nucleotide sequence of RNA
• -converted (translated) into
• amino acid sequence of
• polypeptides
• -translational machinery
• (ribosomes and tRNAs)
• conserved in all life forms
• -polypeptides, composed of
• 20 different aminoacids, are
• folded into mature proteins
• All life forms descent from the same ancestor

multiple proteins
multiple proteins
multiple proteins
5
LAST COMMON ANCESTOR, LCA possessed -DNA-based
genetic code and its transcription
mechanism -translation machinery (ribosomes,
tRNAs) -biosynthethesis of amino
acids -protein-based enzymes -membranes -energy
transfer and conversion reactions -several
metabolic and catabolic pathways
6
LIFE BEFORE THE LCA -- THE RNA WORLD
Evolution of the genetically coded protein
synthesis REQUIRED THE PRE-EXISTENCE OF THE
RNA-BASED TRANSLATION MACHINERY -ribosomes
-tRNAs -maybe, in interaction with RANDOM
polypeptides or co-factors? -maybe
catalysed by inorganic templates ...??
Accumulation of the central RNA components
required replication RNA-dependent RNA
replication ----
REPLICATION gt selection gt evolution gt LIFE
?????
OR, AT LEAST, POTENTIAL FOR LIFE
7
The early replicons -were heterotrophic
(Oparin-Haldane Heterotrophic Hypotheses) -had no
cell membranes -had no protein coding capacity,
neither protein translation machineries gt no
protein catalysis was available gt the early
replicons were catalytic RNAs, or RNA-like
molecules Functions mediated by RNA sequence and
secondary structures --i.e. by RNA-RNA base
pairing, transesterification, nucleophilic attack
by the 2-O, hydrolysis....
8
Known catalytic activities of ribozymes
-self-cleavage or ligation via transesterification
- 2-3 cyclic phosphates (hammerhead and
hairpin ribozymes) -self-splicing via
transestrification -3- 5 phosphodister bonds
(group I and II introns) -trans RNA-splicing
via transestrification -3- 5 phosphodister
bonds (splicesomes) -pre-tRNA processing via
hydrolysis (3 -OH) Rnase P -peptidyl transfer
(peptide bond formation) (Ribosome)
-functions mediated with minimal complexity
minimal RNA-RNA interactions (smallest natural
ribozyme 40 nts, artificial 29 nts)
-functions in cis, and in trans gt Molecular
ecosystems with different interacting components
Potential for evolution of genetic code
9
Relicts of early replicons ??
ribosomes early translation even earlier
replication machineries tRNA tags for
RNA-genome replication, genome telomers
-still used as such
splicesomes, group II and group I introns gt
mRNA maturation Rnase P gt tRNA
maturation snoRNAs gt rRNA maturation other
non-coding (nc) RNAs gt e.g. translational
arrest ....
Viroids autocatalytically cleaved non-coding
RNAs RNA viruses small RNAs which function as
genomes, and as translation templates (mRNAs)
10
Viroid replication by rolling circle system,
with autocatalytic cleavage by the hammerhead
structure
Hammerhead structure of Avocado sun blotch viroid
11
Viruses resemble early replicons -semi-living
entities replicate only in environments where
they are complemented for necessary functions and
compounds fully heterotrophic for their
building units -composed of one (or few) simple
polymers nucleic acid (and protein) -code for
only one (or a few) essential functions
replication -use simple RNA-structures for
efficient functions and recognition sites -for
replication initiation -for translation
initiation -for maintenance of RNAs -viruses
replicate and evolve efficiently ---
12
Efficient replication initiation mechanisms
tRNA-mimicry - relicts of the genome tags of
early life?
tRNA structure, in molecular and in schematic
form
Schematic pictures of the TYMV 3 end (on the
left), and of the canonical tRNA
... in several viruses (TYMV, TCV, Qß-phage) the
CCA-polynucleotide is adequate for replication
initiation
13
Utilization of the tRNA-tag or primer in extant
genomes
-in 3 end of many RNA-viruses
14
Simple translation initiation and regulation
mechanisms
-initiation in a cap-independent fashion,
regulated by simple (in some cases) RNA
sequences -regulation by long-distance RNA-RNA
interactions...
15
RNA-recombination means to increase genome size
and complexity, and to re-assemble damaged
(fragmented) genomes
Mechanisms -template switching (RNA-polymerase
jump to new template), -cleavage / ligation,
trans-esterification (autocatalytic??) -occurs
commonly among RNA-viruses -specific example
hybrid of viroid and host mRNA gt Delta
hepatitis virus
16
Means for RNA stability
1. Viroids Stable secondary structure
17
Viruses in evolution of life From RNA to DNA ??
-RNA genomes can convert into DNA (via reverse
transcription) -virus-like elements
(retroelements, DNA viruses) can integrate into
DNA genomes and transduce DNA most efficient
transfer of genetic material between species
... -eukaryotic genomes are largely composed of
retroelements gt cellular genomes can be of viral
origin -linear, fragmented (eukayote-like)
genomes are more ancestral than prokaryotic
genomes, e.g. the LCA was of eukaryotic-type
(Poole et al. 1998)
18
PROBLEMS OF RNA REPLICONS ORIGINS -heterotrophy
dependency on the surrounding molecular
ecosystems for all building components, energy
and translation machinery WHERE ON EARTH COULD
IT EXIST ??? WHAT CONDITIONS CAN SUPPORT FULL
HETEROTROPHY?? -chirality -compartmentalization?
OTHER PROBLEMS Poor polymerization activity of
ribozymes ???? Stability Adequate Size
Selection Accumulation
19
Problems in assembly of nucleotides and of
oligonucleotides
Joyce 2002, Nature 418214
20
Chemical complexity and instability of
ribonucleotide-polymers maybe simpler
nucleotide-analoques were used ??
Joyce 2002, Nature 418214
... RNA-like molecules with more simple structure
e.g. Threose-NAs, Peptide-NAs, Glycerol-NAs, or
Pyranosyl-NAs
-The first heritable information was imbedded in
the structure (or sequence) of these replicating
molecules convertable to RNA
21
conditions for producing the building blocks ...

• starting material simple inorganic molecules
• (HCN, CH2O, NH3, CH4, H2O, H2)
• gt pre-biotic synthesis of nucleotide bases,
• amino acids in high-energy conditions
• Problems
• synthesis of ribose, assembly of nucleosides?
• conditions for polymerisation??
• Problems
• spontaneous assembly into polymers?
• into autocatalytically replicating molecules?
• high-energy conditions degrade polymers !!!

22
ORIGIN OF LIFE IN BLACK SMOKERS ?
adapted from Martin and Russell 2002
23
Possible conditions for prebiotic chemistry
M42M43, Giant molecular cloud in Orion
24
comets and asteroids as potential sources of
prebiotic materials
25
icy environments
RNA reactions in ice -more effective
polymerization of nucleotides -more effective
ligation by ribozyme ligase (hairpin)
Comet Hale-Bopp, 1997
26
Pleiades and Comet Machholz, 2005-01-07(A. and
H. Lehto)