The Genetic Code Metabolism Clay. A complete theory for the Origin of Life

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1 The Genetic Code Metabolism Clay A complete theory for the Origin of Life

5 Genetic Code G C A U C G A U G A C U G A C U G A C U G A C U Gly Ala Pro Arg Thr Ser Val ILeu Leu Glu Asp Gln Hist Lys Asn Arg Ser Leu Phe Term Cys Term Tyr Met Trp

6 Genetic Code G C A U G C A U Gly G A C U G A C U G A C U G A C U

7 Genetic Code G G C A U Gly Ala G A C U C Arg Pro G A C U A G A C U U G A C U

8 Genetic Code G C A U G Gly Ala Glu Asp G A C U C Arg Pro Gln Hist G A C U A Arg Ser Thr Lys Asn G A C U U G A C U

9 Genetic Code G C A U C G A U G A C U G A C U G A C U G A C U Gly Ala Pro Arg Thr Ser Val ILeu Leu Glu Asp Gln Hist Lys Asn Arg Ser Leu Phe Term Cys Term Tyr Met Trp 1

10 . Origins of Life (1975)

12 Genetic Code G C A U C G A U G A C U G A C U G A C U G A C U Gly Ala Pro Diapr Thr Ser Val ILeu Leu Glu Asp Gln Hist Diapr Asn Diapr Ser Leu Phe Term Cys Term Tyr Met Trp

14 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 takeover of the control machinery by organic macromolecules-a genetic metamorphosis-is then considered to have occurred. J. Theoret. Biol. (1965) 10, 53-88

15 J Mol Evolution 4, (1975) Metabolism

20 Amino acid biogenesis, evolution of the genetic code and aminoacyl-trna synthetases Liron Klipcan, Mark Safro Journal theor Biol 228(2004)

21 Origin of Life and Photosynthesis

22 Photosynthesis

23 Photosynthesis and the origin of life.: Origins of Life and the Biosphere 1998, 28(4-6): Abstract. The origin of life is considered to have occurred in a hot spring on the outgassing early earth. The first organisms were self-replicating iron-rich clays which fixed carbon dioxide into oxalic and other dicarboxylic acids. This system of replicating clays and their metabolic phenotype then evolved into the sulfide rich region of the hot spring acquiring the ability to fix nitrogen. Finally phosphate was incorporated into the evolving system,which allowed the synthesis of nucleotides and phospholipids. If biosynthesis recapitulates biopoesis, then the synthesis of amino acids preceded the synthesis of the purine and pyrimidine bases. Furthermore the polymerization of the amino acid thioesters into polypeptides preceded the directed polymerization of amino acid esters by polynucleotides. Thus the origin and evolution of the genetic code is a late development and records the takeover of the clay by RNA. Conclusion It there was no soup and life began as a photoautotrophic iron rich clay on Earth, then when we sample the surface of Mars for fossils of early life. We should look not only for amino acids and other biochemicals but also for the ancient fossil minerals such as iron-rich clays and magnetite

24 The Origin and Evolution of the Genetic Code

25 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.

26 The Cold Spring Harbor Meeting The Evolution of the Translational apparatus and its implications for the origin of the Genetic Code

27 Starting with the ribosome Nucleotide transferases

28 The Ribosome

31 A hierarchial model for evolution of 23S ribosomal RNA K Bobkov and S V Steinberg Nature 457p (2009)

32 Peeling the Onion: Ribosomes are Ancient Molecular Fossils C Hsiao et al Mol.Biol.Evol (2009)

34 History of the Ribosome and the origin of translation A Petrov et al PNAS vol 112 p (2015)

35 Ribosomal Proteins

36 Boston University BMERC Temple Smith Graduate students Prashanth Vishnwanath Paola Favaretto University of Texas at Austin Robin. R. Gutell Graduate student Jung.C.Lee

39 The ribosomal protein Likely played critical role In early structures. And they still do in subunit assembly

44 The summary of this meeting involves the simple idea that the translational system evolved out a world of small peptides and polynucleotides.

45 The Aminoacyl-tRNA Synthetases

Most trna synthetase have three domains.

48 They must recognize both the correct amino acid and its cognate trna; two molecular recognition codes. Most trna synthetase have three domains. As a side note, Jakubowski Showed that a few of these can transfer to a Thioester trna Amino acid Anti-codon binding

50 C N

52 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.

54 , 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 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.

55 Thioester World

58 What can an organism do? What can a biosphere do?

59 The Seed CO 2,H 2 0,HCO - 3,H 2 S, N 2,NH 3, CH 2 O, CH 3 CHO

60 Can we use this algorithm to learn about the history of metabolism? Starting from a ~10,000 metabolite network (KEGG)?

61 The phosphate-free core network counts 260 metabolites and 315 reactions

62 Implications 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 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 What other messages are hidden in metabolism? Is biopolymer-independent inheritance possible? How many dots are we missing?

64 The Evolution of the trna The Origin of the RNA province

66 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 trna Origins of Life 14, (1984) p

67 The CCA enzyme

68 D61 D110 N C Extracted 2D Topological secondary structure E96 Crystal structure from, Xiong and Steitz 2004

69 D61 D110 trna N E96 2D Topological secondary structure with active site residues marked in red C From crystal structure, Figure 2 in Xiong and Steitz 2004

70 Possible early assembly of CCA enzyme core from short peptides D61 D110 N Inserted E96 C Simple beta Hairpin Beta-alpha-beta Plus

73 The Operational Code

75 Four Primordial modes of trna-synthetase recognition determined by the (GC) operational code. Sergei N Rodin and Susumu Ohno PNAS 94 p (1997 The Early (G,C) Code In contrast with anticodons (and also codons), which are built of four bases, G, A, C, and U, their double-stranded precursors in the positions of acceptors appear as triplets almost invariably composed of G-C and C-G base pairs. The archaic (G,C) code was hypothesized long ago. The general thesis has 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 pairs strongly supports this hypothesis.

78 Class II synthetase expansion Addition of Editing domain Mini RNA Helix? Or only XCCA? Expanded Operational reading Addition of Anti codon domain

79 Potential active site operational code interactions Dividing the class II into two groups 1H4T Bac Pro

81 trnas Discriminator base Operational code Anticodon Proc Natl Acad Sci U S A May 13; 94(10): Four primordial modes of trna-synthetase recognition, determined by the (G,C) operational code Sergei N. Rodin and Susumu Ohno

82 Our current ideas derive from the work of many others, in particular, those attending the recent Cold Spring Harbor meeting

1. DNA, RNA structure. 2. DNA replication. 3. Transcription, translation

1. DNA, RNA structure. 2. DNA replication. 3. Transcription, translation 1. DNA, RNA structure 2. DNA replication 3. Transcription, translation DNA and RNA are polymers of nucleotides DNA is a nucleic acid, made of long chains of nucleotides Nucleotide Phosphate group Nitrogenous