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The Genetic Code –MetabolismClay
A complete theory
for the Origin of Life
1971-2016
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Genetic Code
G
C
A
U
CG A UG
A
C
U
G
A
C
U
G
A
C
U
G
A
C
U
Gly Ala
ProArg
Thr
Ser
Val
ILeu
Leu
Glu
Asp
Gln
Hist
Lys
Asn
Arg
Ser
Leu
PheTerm
Cys
Term
Tyr
Met
Trp
-
Genetic Code
G
C
A
U
CG A UG
A
C
U
G
A
C
U
G
A
C
U
G
A
C
U
Gly
-
Genetic Code
G
C
A
U
CG A UG
A
C
U
G
A
C
U
G
A
C
U
G
A
C
U
Gly Ala
ProArg
-
Genetic Code
G
C
A
U
CG A UG
A
C
U
G
A
C
U
G
A
C
U
G
A
C
U
Gly Ala
ProArg
Thr
Glu
Asp
Gln
Hist
Lys
Asn
Arg
Ser
-
Genetic Code
G
C
A
U
CG A UG
A
C
U
G
A
C
U
G
A
C
U
G
A
C
U
Gly Ala
ProArg
Thr
Ser
Val
ILeu
Leu
Glu
Asp
Gln
Hist
Lys
Asn
Arg
Ser
Leu
PheTerm
Cys
Term
Tyr
Met
Trp
1
-
.
Origins of Life 3 423-7 (1975)
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Genetic Code
G
C
A
U
CG A UG
A
C
U
G
A
C
U
G
A
C
U
G
A
C
U
Gly Ala
ProDiapr
Thr
Ser
Val
ILeu
Leu
Glu
Asp
Gln
Hist
Diapr
Asn
Diapr
Ser
Leu
PheTerm
Cys
Term
Tyr
Met
Trp
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The Origin of Life and the Nature of the Primitive Gene
A.G. CAIRNS-SMITH Chemistry Department, The University of Glasgow,Glasgow, W.2, Scotland
According to the specific theory that is proposed, the primitive genographs were patterns of substitutions in colloidal clay crystallites. (The theoretical information density in such a crystallite is comparable to that in DNA.) Evolution proceeded through selective elaboration of substitutional genographs that had survival value for the clay crystallites that held them (at first through genetically controlled adsorption of a “spectrum” of organic molecules) within a complex, dynamic, primitive environment. A gradual “take-over” of the control machinery by organic macromolecules-a genetic metamorphosis-is then considered to have occurred.
J. Theoret. Biol. (1965) 10, 53-88
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Metabolism
J Mol Evolution 4,359-370 (1975)
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Amino acid biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetasesLiron Klipcan, Mark Safro
Journal theor Biol 228(2004) 389- 396
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Origin of Life and Photosynthesis
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Photosynthesis
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•
• Photosynthesis and the origin of life.:
• Origins of Life and the Biosphere 1998, 28(4-6):515-521
• Abstract
• . The origin of life is considered to have occurred in a hot spring on theoutgassing early earth. The first organisms were self-replicating iron-richclays which fixed carbon dioxide into oxalic and other dicarboxylic acids.This system of replicating clays and their metabolic phenotype thenevolved into the sulfide rich region of the hot spring acquiring the ability tofix nitrogen. Finally phosphate was incorporated into the evolving system,which allowed the synthesis of nucleotides and phospholipids. Ifbiosynthesis recapitulates biopoesis, then the synthesis of amino acidspreceded the synthesis of the purine and pyrimidine bases. Furthermore thepolymerization of the amino acid thioesters into polypeptides preceded thedirected polymerization of amino acid esters by polynucleotides. Thus theorigin and evolution of the genetic code is a late development and recordsthe takeover of the clay by RNA.
• Conclusion
• It there was no soup and life began as a photoautotrophic iron rich clay onEarth, then when we sample the surface of Mars for fossils of early life. Weshould look not only for amino acids and other biochemicals but also forthe ancient fossil minerals such as iron-rich clays and magnetite
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The Origin and Evolutionof the Genetic Code
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• In 1968 Crick stated:
• “It is almost impossible to discuss the origin of the code without discussing the origin of the actual biochemical mechanisms of protein synthesis. This is very difficult for two reasons: it is complex and many of its details are not yet understood.”
•
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The Cold Spring Harbor Meeting
• ‘The Evolution of the Translational apparatus and its implications for the origin of the Genetic Code”
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Starting with the ribosome
Nucleotide transferases
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The Ribosome
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A hierarchial model for evolution of 23S ribosomal RNAK Bobkov and S V SteinbergNature 457p 977-980 (2009)
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Peeling the Onion: Ribosomes are Ancient Molecular FossilsC Hsiao et alMol.Biol.Evol. 26 2415-2425 (2009)
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History of the Ribosome and the origin of translationA Petrov et alPNAS vol 112 p 15396-15401 (2015)
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Ribosomal Proteins
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Boston University BMERC
Temple Smith
Graduate studentsPrashanth VishnwanathPaola Favaretto
University of Texas at Austin
Robin. R. Gutell
Graduate studentJung.C.Lee
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The ribosomal proteinLikely played critical roleIn early structures.
And they still do in subunitassembly
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• The summary of this meeting involves
the simple idea that the translational
system evolved out a world of small
peptides and polynucleotides.
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The Aminoacyl-tRNA Synthetases
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tRNA
Anti-codonbinding
They must recognize both the correct amino acid and its cognate tRNA; two molecular “recognition codes”. Most tRNA synthetase have three domains.
Amino acid
As a side note, JakubowskiShowed that a few of these can transfer to a Thioester
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4 55
N
C
276 35
4
-
abstract
Class II Aminoacyl-tRNA synthetases are a set of very ancient multi domain proteins. The evolution of the catalytic domain of Class II synthetases can be reconstructed from three peptidyl-hairpins. Further evolution from this primordial catalytic core leads to a split of the Class II synthetases into two divisions potentially associated with the operational code. The earliest form of this code likely coded predominantly Glycine (Gly), Proline (Pro), Alanine (Ala) and ‘‘Lysine”/Aspartic acid (Lys/Asp). There is a paradox in these synthetases beginning with a hairpin structure before the Genetic Code existed. A resolution is found in the suggestion that the primordial Aminoacyl synthetases formed in a transition from a Thioester world to a
Phosphate ester world.
-
,
Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis
Marko Mociboba, et al
PNAS ∣ August 17, 2010 ∣ vol. 107 ∣ no. 33 ∣ 14585–14590
The enzymatic activity of a SerRS homologs is reminiscent of adenylation domains in nonribosomal peptide synthesis, and thus they represent an intriguing link between programmable ribosomal protein biosynthesis and template-independent nonribosomal peptide synthesis.
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Thioester World
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What can an organism do? What can a biosphere do?
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The Seed
CO2,H20,HCO-3,H2S, N2 ,NH3, CH2O, CH3CHO
-
?
Can we use this algorithm to learn about the history of metabolism? Starting from a ~10,000 metabolite network (KEGG)
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The phosphate-free core network counts 260 metabolites and 315 reactions
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Implications…
Is this the fossil? A rich metabolism may have been present before phosphate, preparing the ground for a phosphate “explosion” and the rise of RNA and proteins
A phosphate-free network is hidden in present-day metabolism, detectable only by looking beyond organismal boundaries
The phosphate-free network is enriched with properties consistent with what we know about early metabolism, and highlights the key role of Fe-S
What other messages are hidden in metabolism?Is biopolymer-independent inheritance possible?How many “dots” are we missing?
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The Evolution of the tRNA
The Origin of the RNA province
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The modern t-RNA is a "tetramer" of a "monomer”(arm and
loop structure) and it is in the loop that the evolution of t-
RNA can be followed. Balasubramanian suggested that the
anti-codon loop structure 5,U...A3, was the earliest t-RNA.
In this paper we speculate that the pentamer structure was
preceded by UGCA, UGGA, UCCA and UCGA. It is further
postulated that these ancient t-RNAs were preceded by
UGC, UGG, UCC and UCG.
Speculations on the evolution of the Genetic Code III: The Evolution of tRNAOrigins of Life 14, (1984) p 643-648
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The CCA enzyme
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N
C
21
453
1’
D6
1
E96
D11
0
1
2
3
4
4
55
Crystal structure from, Xiong and Steitz 2004
Extracted 2D Topological secondary structure
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N
C
21 453
1’D
61
E96
D110
From crystal structure,
Figure 2 in
Xiong and Steitz 2004
2D Topological secondary
structure with active site
residues marked in red
tRN
A
-
N
C
24
53
D61
E96
D11
0
Inserted
Simple beta Hairpin
Beta-alpha-beta Plus
Possible early assembly of CCA enzyme
core from short peptides
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The Operational Code
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Four Primordial modes of tRNA-synthetase recognitiondetermined by the (GC) operational code.
Sergei N Rodin and Susumu OhnoPNAS 94 p 5183-5188 (1997
The Early (G,C) Code In contrast with anticodons (and also codons), which are built offour bases, G, A, C, and U, their double-stranded precursors inthe 1-2-3 positions of acceptors appear as triplets almost invariablycomposed of G-C and C-G base pairs.
The archaic (G,C) code was hypothesized long ago . The general thesishas been argued that, like all other evolving systems, the code
“began simply and evolved to the present complexity’’ .The very fact that the anticodon/codon-like triplets in the acceptor
helix turned out to be composed of predominantly G-C and C-G base pairsstrongly supports this hypothesis.
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Class II synthetase expansion
Addition ofAnti codondomain
Expanded Operationalreading
Addition ofEditing domain
Mini RNA Helix ? Or onlyXCCA ?
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1H4T Bac Pro
Potential active site operational code interactionsDividing the class II into two groups
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Proc Natl Acad Sci U S A. 1997 May 13; 94(10): 5183–5188.Four primordial modes of tRNA-synthetase recognition, determined by the (G,C) operational codeSergei N. Rodin and Susumu Ohno
tRNAsDiscriminator base
Operational code
Anticodon
https://www.ncbi.nlm.nih.gov/pubmed/?term=Rodin SN[Author]&cauthor=true&cauthor_uid=9144212https://www.ncbi.nlm.nih.gov/pubmed/?term=Ohno S[Author]&cauthor=true&cauthor_uid=9144212
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Our current ideas derive from the work of many others, in particular,those attending the recent Cold Spring Harbor meeting
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