The Coevolution of Biomolecules and Prebiotic Information Systems in the Origin of Life: A Visualization Model for Assembling the First Gene

Abstract

Prebiotic information systems exist in three forms: analog, hybrid, and digital. The Analog Information System (AIS), manifested early in abiogenesis, was expressed in the chiral selection, nucleotide formation, self-assembly, polymerization, encapsulation of polymers, and division of protocells. It created noncoding RNAs by polymerizing nucleotides that gave rise to the Hybrid Information System (HIS). The HIS employed different species of noncoding RNAs, such as ribozymes, pre-tRNA and tRNA, ribosomes, and functional enzymes, including bridge peptides, pre-aaRS, and aaRS (aminoacyl-tRNA synthetase). Some of these hybrid components build the translation machinery step-by-step. The HIS ushered in the Digital Information System (DIS), where tRNA molecules become molecular architects for designing mRNAs step-by-step, employing their two distinct genetic codes. First, they created codons of mRNA by the base pair interaction (anticodon-codon mapping). Secondly, each charged tRNA transferred its amino acid information to the corresponding codon (codon-amino acid mapping), facilitated by an aaRS enzyme. With the advent of encoded mRNA molecules, the first genes emerged before DNA. With the genetic memory residing in the digital sequences of mRNA, a mapping mechanism was developed between each codon and its cognate amino acid. As more and more codons 'remembered' their respective amino acids, this mapping system developed the genetic code in their memory bank. We compared three kinds of biological information systems with similar types of human-made computer systems.

Keywords: AnyLogic visualization of encoding mRNAs by tRNAs; analog information; coevolution of biomolecules and information systems; digital information; hybrid information; hydrothermal crater lakes; memory transfer and memory bank; peptide/RNA world; prebiotic information systems; the genetic code.

Figure A1

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Figure A2

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Figure A3

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Figure 1

(A) the hierarchical origin of life, viewed as five ascending stages of increasing complexity, showing the biomolecules in the prebiotic world that led to the development of the first cells. These are the cosmic, geological, chemical, information, and biological stages—each higher-level acquired novel emergent properties. In the dark hot environments of hydrothermal crater lake basins, prebiotic synthesis led to first life. (B) the three ways of processing information in life are analog, hybrid, and digital, shown against the hierarchy of life.

Figure 2

Cradle of life and its information system. Hydrothermal crater lakes in the Early Archean offered a protective haven for prebiotic synthesis. The boiling water was rich with building blocks of life. On the surface crater basin, lipid vesicles and hydrocarbons were buoyant like tars. The mineral substrates on the floor of the basin acted as catalytic surfaces for the concentration and polymerization of monomers. Convection currents thoroughly mixed the bubbling biotic soup. Some lipid vesicles by convective current went down to the crater floor and stuck to the mineral substrate, encapsulating biopolymers such as RNA and peptides. Hydrothermal vents provide heat, gases, and chemical energy, including thioester and ATP molecules.

Figure 3

Chiral selection of monomers such as L-amino acids and D-ribose sugar from the racemic mixture on the mineral substrate floor of the hydrothermal crater vent environment. A short chain of the peptide can be formed by linking a few L-amino acids to each other via peptide bonds by condensation reaction. L-amino acids become monomers of proteins. On the other hand, D-ribose joins with a phosphate molecule to form the backbone of a nucleobase; these three molecules join to form a nucleotide, the monomer of RNA.

Figure 4

Amphiphilic compounds like fatty acid can self-assemble into cell-sized vesicles bounded by a membrane. (A) the polar simple fatty acid was likely a major component of the early prebiotic cell membrane due to its ability to form a vesicle. It has a hydrophilic head and a hydrophobic tail. (B) as a monolayer, a micelle can only trap oils, not water, and thus cannot be a precursor to the cell. A bilayer vesicle that trapped water and water-soluble molecules must have given rise to the cell membrane.

Figure 5

Condensation reaction on mineral surfaces, where activated monomers drive endergonic polymerization reactions; (A) amino acid structure; all amino acids have the same general configuration: a central carbon bonded to an amino acid functional group, a carboxyl functional group, a hydrogen atom, and a side chain, or R-group. (B–D) How amino acids polymerize to form polypeptides by peptide bonds; (B) the resemblance of an amino acid to a fish helps differentiate its parts. The three amino acids chosen as examples are incredibly similar: each possesses a carboxylic acid group (the ‘tail’) and an amino group (the ‘head’). However, they differ in the ‘dorsal fin’ (R-group of amino acid), which determines the kind of amino acid (here, alanine, glycine, and serine). (C) three molecules of amino acids can polymerize into a polypeptide by linking the amino group of one with the carboxylic acid group of another. This reaction forms a water molecule through the combination of a hydrogen ion (H⁺) discarded from the carboxyl group and a hydroxyl group (OH^_) discarded from the amino group). (D) shows how a longer chain of amino acids (i.e., a polypeptide) can be formed by removing a water molecule from each link; mRNA-directed protein molecule is also formed similarly by linking amino acids in ribosome during translation. (E) nucleotides can join into an RNA molecule by linking the sugar (S) and phosphate (P) molecules with the backbone of the ribonucleotide bases (B). (E) the linking of nucleotides into RNA was accomplished by dehydration; (F) shows the three components of a nucleotide (phosphate group, sugar, and nitrogenous base) in more detail.

Figure 6

Two possible models of the encapsulation of polymers by simple fatty acid membranes on the mineral surface. In model (A), both RNAs and polypeptides are brought together in the same vesicle. In model (B), RNA and peptides are encapsulated separately on the crater basin, then fused in the aqueous environment.

Figure 7

Primitive protocell enclosing assemblages of peptide and RNA molecules. (A) Encapsulated polymers such as peptides and RNA and prebiotic soup to create primitive cytoplasm. (B) Some peptides were inserted into the lipid bilayer to enhance permeability in the protocell. The peptides would produce ion-conducting channels through the bilayers that allow phosphate, thioester, ATP, and other nutrients such as amino acids to enter the cell. Molecular crowding inside primitive cytoplasm would encourage symbiotic relations between peptides and RNAs.

Figure 8

Fusion and fission of lipid bilayers with inserted peptide molecule (see Figure 7 for explanation). The peptide channels allowed nutrients, lipid components, and energy from the environment to enter protocells by diffusion for growth and division. These protocells form flexible, semi-permeable vesicles, capable of dividing into two such daughter vesicles or of joining with another without any moment of losing their structural continuity. Unlike living cells, the division of protocells is asymmetric, where daughter cells might inherit an unequal amount of cytoplasmic content. The transfer of information from parent to daughter cells is vertical. The cellular division of first cells inherited this property of protocells, but DNA replication created identical daughter cells.

Figure 9

Hierarchical evolution of the Analog Information System (AIS) in the early stage of peptide/RNA world. The most basic AIS is termed ‘Molecular Preference AIS’. The higher-level stage AIS is built upon the lower-level AIS. For example, the next stage of AIS, the wet–dry AIS, subsumes the molecular preference AIS, and so on.

Figure 10

(A) replication of an RNA molecule by base-pairing. Left: the original RNA strand acts as a template to make a complementary strand by base-pairing. Right: this complementary RNA strand itself acts as a template, forming an RNA strand of the original sequence. (B) Although RNA is a single-stranded molecule, it can form a secondary hairpin structure of ribozyme. (C) Hammerhead ribozyme, like protein, can create tertiary structures and catalyze reactions; the tertiary structure can have both Watson–Crick and non-canonical base pairs.

Figure 11

The origin of three components of translation machinery from the hairpin structure of ribozyme with a stem and loop: pre-tRNA molecules (A–D), bridge peptide (E), and ribosome (F). (A,B) The hairpin structure of two ribozymes, each with a loop and a stem. (C) The ligation or duplication of the hairpin structures may give rise to a double hairpin structure, forming a T-hairpin loop and D-hairpin loop with an anticodon (ANT) site between the two stems. (D) A schematic, simplified diagram of the pre-tRNA molecule showing the anticodon site and amino acid attachment site. (E) The hairpin ribozyme structure with a stem and loop and its activating enzyme, the bridge peptide. The amino acid is attached to its free oligonucleotide end by the bridge peptide. (F) Ribosome, a hybrid ribonucleoprotein complex, decodes the message of mRNA to synthesize a small protein chain. It is a decoder of digital information to analog information (modified from [40]).

Figure 12

(A) The evolution of a tRNA molecule from a precursor pre-tRNA molecule (A,B) by gene duplication. (C) The secondary structure of a tRNA molecule could have been created by ligation of two half-sized pre-tRNA structures. Now a full-length tRNA structure looks like a cloverleaf; its anticodon end forms a complementary base pair with the codon of mRNA; (D) a simplified and schematic diagram of the tRNA molecule showing the site of the anticodon. (E) The cloverleaf secondary structure of tRNA could be folded into an L-shaped tertiary structure; it shows the aminoacylation site at the CCA end. The minihelix region (half domain of tRNA with the amino acid attachment site) interacts with the conserved domain of aaRS for amino acid activation. The other half of tRNA interacts with the non-conserved domain of aaRS for specific recognition of an anticodon (modified from [40]).

Figure 13

Hierarchical emergence of Hybrid Information System (HIS) during the early stage of peptide/RNA world. The most basic HIS is termed ‘RNA Template HIS’. The higher level (stage) HIS is built upon the lower level HIS. For example, the next stage HIS, the Ribozymal HIS, subsumes the RNA template HIS and so on.

Figure 14

Creation of codons by pre-tRNA molecules step by step. (A) GADV amino acids govern the origin of codons via pre-tRNAs; anticodon of a pre-tRNA molecule hybridizing with the corresponding nucleotide available in the prebiotic soup to form a codon strand; each codon developed a memory for a specific amino acid. The four amino acids, glycine (G), alanine (A), aspartic acid (D), and valine (V), were available in the abiotic stage. (B) Codons, thus created by pre-tRNAs, began to link to form a strand of pre-mRNA with coding sequence; (C) Pre-tRNA and pre-mRNA interactions generated rudimentary translation. In this figure, we offer a specific mapping mechanism between codons and their cognate amino acids that led to rudimentary translation and the genetic code (modified from [40]).

Figure 15

The encoding properties of tRNA. tRNA played two critical roles in creating and encoding codons corresponding to two different genetic codes. First, it created a codon by Watson–Crick base pair interaction (anticodon–codon mapping). Secondly, each charged tRNA transferred its amino acid information to the corresponding codon (codon–amino acid mapping). Participation of aaRS in the recognition process is an attractive possibility.

Figure 16

A four-level hierarchy of Digital Information System (DIS) stages in the peptide/RNA world. The codon reader-acceptor DIS was able to form a codon. The sequence, a memory-based DIS in the next stage, was able to link codons into pre-mRNAs. The codons in pre-mRNA and mRNA were encoded by pre-tRNA and tRNA, respectively. Finally, mRNA was decoded by translation machine to create protein chain.

Scheme 1

Twenty primary amino acids in the Genetic Code and their corresponding numerical codons shown by 23 alphabets. This represents the decoding table from mRNA to protein translation. The three letters B, O, and U remain unused.

Scheme 2

Universal Genetic code showing numerical codons with corresponding amino acids.

Scheme 3

Codon–amino acid mapping in three stages of genetic code using CATI software. In SNS and universal genetic code, the sequence of generating redundancy of codons to amino acids is shown.

Figure 17

Codon–amino acid mapping and the origin of genes. Encoding codons by charged pre-tRNA and tRNA molecules in the three stages of the genetic code, controlled by the availability of amino acids in hydrothermal crater vent environment. In the GNC code, four pre-mRNA codons specify the four amino acids. In the SNS code, 16 mRNA codons code ten amino acids. In the universal genetic code, 61 mRNA codons designate the 20 amino acids. In the left column of each stage, the white circles represent the uncoded codons, while the blue codons represent encoded codons. Twenty-three to forty-five charged tRNA molecules perform the task of encoding codons.

Figure 18

The coevolution of translation machines and the genetic code in three stages: (A) encoding of pre-mRNA molecule by pre-tRNA/pre-aaRS translation machine when GNC code evolved; (B) encoding of short-chain mRNA molecule by tRNA/aaRS translation machine when SNS code appeared; and finally, (C) encoding of long-chain mRNA by tRNA/aaRS/ribosome machine when universal code evolved. With the improvement of the translation machine, the information density of mRNA also increased (modified from [40]).

Figure 19

(A) (top) Three stages of the evolution of mRNA, translation machines, and genetic code. (a) Decoding of pre-mRNA by pre-tRNA/pre-aaRS machine resulting in the primitive GNC code. (b) Fecoding of short-chain mRNA by tRNA/aaRS machine in the transitional SNS code. (c) Decoding of long-chain mRNA by tRNA/aaRS/ribosome machine in the universal genetic code. Left column of the diagram shows the recruitment of amino acids during the evolution of the genetic code. (B) (bottom) Darwinian evolution began in the peptide/RNA world, an interplay between digital information and its supporting structure, such as a translation machine. The supporting structure is coupled to the information carrier by rules, such as RNA base-pairing and genetic code. The supporting structure is nourished by the chemicals and energy from the hydrothermal vent environment and provides the information carrier positive feedback.

Figure 20

In a digital information transmission system, mRNA functions as the encoder of amino acid information and ribosome as a decoder of DIS to AIS to create protein.

Scheme 4

Three stages of the DIS, HIS, and AIS during the evolution of the genetic code. In GNC code, pre-mRNA was decoded by a pre-tRNA/pre-aaRS translation machine, creating a polypeptide chain. In SNS code, short-chain mRNA was decoded by a tRNA/aaRS machine, producing short-chain protein. In universal genetic code, long-chain mRNA was decoded by tRNA/aaRS/ribosome machine, manufacturing long-chain protein.

Scheme 5

(A) Universal genetic code table shows 64 codons, each corresponding to a specific amino acid or stop signal. The start codon (AUG) is shown in green. Stop codons (UAA, UAG, and UGA) are shown in red. (B) In the genetic code, 20 amino acids are used in protein synthesis showing corresponding codons in redundancy.

Figure 21

A Block diagram of the TR-10 analog computer built by Electronic Associates, Inc. EAI’s PACE TR-10, an electronic analog computer.

Figure 22

Block diagram of a basic digital computer with a uniprocessor CPU. Black lines indicate data flow, whereas red lines indicate control flow. Arrows indicate the direction of flow [adapted from Lambtron-owned work, CC BY-SA 4.0].

Figure 23

Block diagram of an available hybrid computer system.

Figure 24

Coevolution of biomolecules with the biological information systems in the peptide/RNA world. An analog information system dominated the early stage of abiogenesis. With the emergence of nucleotides, hybrid information began to emerge. The origin of pre-mRNA and mRNA marked the digital revolution. During the origin of translation and the genetic code, the directionality of information flow from mRNA to proteins emerged.