Information encoding in the Nucleic Acids through a Dissipation-Replication Relation J. Mejía-Morales1 and K. Michaelian2 Posgrado en Ciencias Físicas, Universidad Nacional Autónoma de México, Cto. de la Investigación Científica, Cuidad Universitaria, C.P. 04510, Mexico1 Instituto de Física, Universidad Nacional Autónoma de México, Cto. de la Investigación Científica, Cuidad Universitaria, C.P. 04510, Mexico2
[email protected] ;
[email protected]
KEYWORDS: Origin of life, origin of codons and amino acids relationship, photonic potential dissipation, increace of entropy, processes out of equilibrium.
Abstract We show how the dissipation of sunlight in organic material leading to its autocatalytic replication provides a mechanism for the accumulation of information nucleic acids. Such a mechanism replaces Darwinian natural selection with a physical-chemical foundation based on entropy production. This mechanism probably operated at the origin of life in the Archean, and still operates today, albeit through complex biosynthetic pathways.
1 Introduction
named “dissipative structures” by Prigogine.
The study of thermodynamics is fundamenetaly based in very strong hipotesys and unreal processes, actually any of the natural processes responds to the thermodynamics because all the natural processes are carried on out of equilibrium.
Life today dissipates the solar photonic potential, the most important source of free energy to dissipate, now and at the time of the origin of life. Every person who had put some thoughts in the origen of life has to acept that the life is very close related whit the Sun light and this is because the inescapable fact that life, like any other irreversible process, requires the dissipation of an external potential to originate, persist, proliferate, and evolve.
In the Clasical Irreversible Thermodynamics (CIT) stablished by I. Prigogine is shown that all the irrevesible processes arise to dissipate an a thermodynamic potential, better understod as a gradient of some potential. The irreversible processes dissipating the thermodynamic potential also increases the entropy production of the system, eventhought if the entropy of the irreversible proces has to reduce its own entropy in order to allow an increace in the entropy production, such structures were
The external potential that life dissipates today is the solar photon potential and the dissipation performed by these pigment molecules when are in a water environment and exposed to the sun’s rays, is the conversion of short wavelength light (UV and visible) into long wave1
2
length light (infrared).
Fundamental molecules (including aromatic amino acids) absorb and dissipate
This solar photonic potential dissipation ocurs at many levels and many scales, from the molecular leve like the organic pigments floating in the sea helping to evaporate water starting the water cycle to hurricans, actually the water cycle itself is a dissipative structur that increases the entropy of the planet, a more dramtic example of this are the hurricans this are a very large dissipative structures that dissipates the thermal energy coming from the solar photonic potential and increse the entropy production of the system Earth.
in the UV-C region.
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Aromatic amino acids have strong affinity to codons (or anti-codons) of DNA and RNA.
There are eight types of affinities between amino acids and nucleotides that form nuclei acids: π−cation bond, stacking of aromatic structures, charge, Van der Waals forces, hidrophobic properties, hidrogen bonds, Nucleotide substitution by amino acids (structural similarity) And the synthesis of amino acids from acids α−ketos bounded to dinucleotides.
1. Without the pre-existence of complicated biosynthetic pathways, the photon potential that life must have dissipated in the Archean was the UV-C, with enough energy to make and break covalent bonds, but not enough to ionize. 2. UV-C component of the solar spectrum indeed arrived at surface of Earth in Archean times, approx 5 W/m ^2. Life was exposed to this potential for at least 1,000 million years (1 Ga).
Of these eight forms of interaction four are random, meaning that the amino acids do not bind to any particular place in the strands of DNA-RNA or the double helix of DNA. But the π−cation bonds, hydrogen bonds, structural similarity and amino acid synthesis from α−keto are not at all random, these interactions link the amino acids almost univocally to either their codons or anticodons. Below we will review some of the most relevant.
3. Fundamental molecules of life (in the three domains) all absorb and dissipate in the UV-C region. 4. Classical Irreversible Thermodynamics (CIT) suggests that systems (molecules) will spontaneously form complexes if this increases the dissipation of the impressed potential. Microscopic dissipative structuring.
3.1 π−cation Bond
5. CIT also suggests that the concentration of a photochemical product will increase much beyond expected equilibrium concentrations if the product acts as a catalyst for dissipating the impressed potential. Proliferation. 6. This leads to a relation between replication and dissipation. 7. Microscopic dissipative structuring is persistent, i.e. structuring remains even after the removal of the impressed potential (due to atomic mobility issues). Information on constructing complexes for dissipation therefore becomes “programmed” in the genome (DNA, RNA) ready to take up dissipation again should the external potential (environment) return to its former state.
3.2
Stacking of aromatic structures
3.3
Hidrophobic properties
3.4
Structural similarity
3.5
synthesis of amino acids
Majerfield y Yarus: Stereochemical theories for the origin of the genetic code propose chemical affinity between amino acid and RNA as the basis for association between codons and/or anticodons and cognate amino acids. Recently, Yarus et al. [Majerfeld and Yarus, 2005] have reviewed the related hypothesis that code assignments origin- ated as part of RNA or RNA-like amino acid binding sites and triplets subsequently ‘escaped’ (took on new functions) to participate as codons and anticodons in a more modern translation apparatus.
8. Point (9.) above implies that the system will evolve to ever greater complexity, up to the biosphere (coupling of biotic with abiotic irreversible processes).
Here, we describe the simplest stereoselective and side chain specific amino acid binding site we have seen, for L-Trp. Notably, this site fits the overall stereochemical pattern.
9. The goal of this article is to describe the information accumulation in the genome (RNA and DNA) through dissipation at the very beginnings of life. 2
The 20 standard biological amino acids are interesting ligands for RNA. They present chemically varied surfaces, and RNAs response to these chemical challenges should be relevant to the intrinsic possibilities of RNA–peptide interfaces [Majerfeld et al., 2005]. Una de las predicciones más importantes del trabajo de Yarus, es que los tripletes afines son inesperadamente frecuentes en los sitios de enlace de los aminoácidos con sus codones afines en el RNA.[Yarus et al., 2009]
precursor were ceded to its more complex products. Soporta la idea de coevolución. The reductive amination that converts a completed α-keto acid into an amino acid is particularly important because it establishes the stereochemical configuration (i.e., L or D) of the amino acid.
[Toulmir et al., 1974]Muestra que existe una afinidad entre aminoácidos aromáticos y oligonucleótidos, tambien es evidenciá y soporte par la UVTAR base de la relación disipación replicación. Muestra como el anillo indólico puede fotocatalizar la separación del dímero de pirimidina. The experiments described above demonstrate not only that the peptide Lys-Trp-Lys binds preferentially to regions containing pyrimidine dimers in UVirradiated DNA, but also that bound peptide molecules are able to photosensitize the splitting of these dimers. The peptide Lys-Trp-Lys binds preferentially to singlestranded regions of a nucleic acid molecule because the stacking of the tryptophyl ring with bases is energetically favored in such regions.
[Majerfeld and Yarus, 2005] Furthermore, stereochemical theories of the origins of the genetic code (Woese et al. 1996) propose that chemical. affinities between codons and/or anticodons and amino acids determined at least some codon assignments. Data exists for eight amino acids, and significant associations were found for both codons and anticodons, In fact, the overall probability of the null hypothesis—that there is no association between these eight kinds of amino acid binding sites and cognate coding triplets—now stands at 5.4 · 10 )11 . This is exceedingly unfavorable to the null hypothesis and in support of a robust relationship between coding triplets and amino acid affinity, especially given that the data include both strongly negative and positive cases. Two histidine anticodons are present in the majority of sequences, GUG in module 1 and AUG in module 2.
The size of the indole ring is similar to that of purine bases so that (1974) the stacking of tryptolhan with DNA bases may involve only one strand of the double helix. Esto puede contribuir a la replicación disipación a mantener las hebras de DNA o RNA flotando en la superficie del agua y decantando las hebras que no tiene afinidad quimica con los aminoácidos Lys-Trp-Lys.
The conserved nucleotides spread over an asymmetrical loop, a terminal loop, and a short stem linking the two. One or both histidine anticodons are present in 86% of the sequences. These nucleotides contribute to binding but substitutions in the middle nucleotide of GUG or the first or second nucleotide in AUG are occasionally observed.
[Dougherty, 2007] Here we present a brief overview of the cation-p interaction. More detailed reviews are available elsewhere. (1–4) We begin with a description of the fundamental nature of the interaction. Exhibe la utilidad del enlace π−cation, en particulas entre los aminoácidos aromáticos (Phe, Tyr, Trp) y la afinidad especial que hay con moléculas que contienen Lys y Arg.
Accordingly, just as for isoleucine (Lozupone et al. 2003; Majerfeld and Yarus 1998) and for tryptophan (Yarus et al. 2005), the simplest and most abundant site for an amino acid contains conserved coding triplets. Therefore, selection for isoleucine, histidine, or tryptophan affinity in RNA-like molecules would have been sufficient to associate se- quences that became coding triplets with the amino acid itself.
[Copley et al., 2005] Codons having U as the second base are associated with the most hydrophobic amino acids, and those having A as the second base are associated with the most hydrophilic amino acids. (de la tabla se observa que los aminoácidos aromáticos empiezan con U). We suggest that both correlations can be explained if, before the emergence of macromolecules, simple amino acids were synthesized from α-keto acid precursors covalently attached to dinucleotides that catalyzed the reactions required to synthesize specific amino acids. The “coevolution” hypothesis [Wong, 1975] suggests that the original genetic code specified a small number of simple amino acids, and that, as more complex amino acids were synthesized from these precursors, some codons that initially encoded a
[Majerfeld and Yarus, 2005] From sequence variation in 50 independent isolates, only 26 bits of information are required to describe this loop (equivalent to only 13 fully conserved nucleotides). Thus, it is among the simplest amino acid binding sites known, as well as selective among hydrophobic side chains. Among site sequences defined as essen- tial to affinity by conservation, protection and modification-interference, there is a recurring CCA sequence (a tryptophan anticodon triplet) which apparently forms one side of the binding site. Such conserved juxtaposition of tryptophan with a cognate coding triplet supports a stereochemical origin for the genetic code. RNA binding sites for 8 of the standard 20 encoded amino acids have presently been 3
isolated and characterized. Here, we describe the simplest stereoselective and side chain specific amino acid binding site we have seen, for L-Trp. Notably, this site fits the overall stereochemical pattern (2). (what Karo said)
α−carboxil siempre están presentes, aportando buenos complementos de los receptores y donadores de los enlaces de hidrógeno.
Other RNAs with a relation to tryptophan have been also reported, often with concurrent affinity for other aromatic amino acids. A stereospecific aptamer for Dtryptophan– Sepharose was isolated by affinity chromatography from a 120 randomized nucleotide region (20), though free amino acid was apparently not an effective ligand. In another selection for L-phenylalanine affinity, the major selected sites accepted tryptophan in addition to the selection target, though with no stereospecificity (21). Another L-phenylalanine affin- ity selection resulted in phenylalanine-specific aptamers as well as a class with general L-aromatic amino acid specificity (22). A mutagenized sequence with affinity for dopamine, when re-selected for tyrosine, yielded three independent L- tyrosine sites that also bound Ltryptophan. Two of these accepted multiple aromatic amino acids, though one of the three moderately discriminated phenylalanine (23). Accord- ingly, RNA can easily specify recognition of aromatic side chains, doing so using differing structures. In light of this history, it is the more notable that the simplest tryptophan site discriminates its ligand from other hydrophobic amino acids, aromatic and linear. The tryptophan anticodon, CCA, appears in one of the two counterloops. It occurs in 20% of total sequences (Figure 9A) and in 14–15 out of 49–53 possible independent isolations of the CYA motif (Table 1). Therefore, just as for L-isoleucine (9,18) and L-histidine (4), selection of tryptophan affinity produces a cognate coding triplet, CCA, as a conserved part of the most easily recurring amino acid binding site. The small size of the active motif suggests in this case that the CCA would be in close proximity to a bound amino acid. The alternative counterloop has a CUA triplet, complementary to UAG, an anticodon triplet which did not enter the standard code as an amino acid. Accordingly, these data support a stereochemical origin for the genetic code for tryptophan, as posited by the escaped triplet theory (2).
[AD et al., 2008, Serganov et al., 2008] Las secciones alifaticas de las cadenas laterales pueden interactuar con las bases nitrogenadas, Sin embargo estas interacciones purínicas base planas- alifáticas son relativamente laxas y no especificas. [Majerfeld and Yarus, 2005] Furthermore, stereochemical theories of the origins of the genetic code (Woese et al. 1996) propose that chemical. affinities between codons and/or anticodons and amino acids determined at least some codon assignments. Data exists for eight amino acids, and significant associations were found for both codons and anticodons, In fact, the overall probability of the null hypothe- sis—that there is no association between these eight kinds of amino acid binding sites and cognate coding triplets—now stands at 5.4 · 10 )11 . This is exceedingly unfavorable to the null hypothesis and in support of a robust relationship between coding triplets and amino acid affinity, especially given that the data include both strongly negative and positive cases. Two histidine anticodons are present in the majority of sequences, GUG in module 1 and AUG in module 2.
The conserved nucleotides spread over an asymmetrical loop, a terminal loop, and a short stem linking the two. One or both histidine anticodons are present in 86% of the sequences. These nucleotides contribute to binding but substitutions in the middle nucleotide of GUG or the first or second nucleotide in AUG are occasionally observed.
[Weber and Lacey, 1978, Hendry et al., 1981]Los aminoácidos con grupos R que pueden formar un par de enlaces de hidrógeno bases de ácidos nucleicos y con pares de bases son Asp,Glu, Asn y Gln. Los posibles esquemas de reconocimiento para residuos cargados son limitados.
[Yarus et al., 2009] The amino acid sites showing strong associations with cognate triplets are chemically varied; basic, polar, aliphatic, and aromatic side chains are detected. 8. Positive triplets do not have any obvious sequence or compositional properties, being AU-rich, GC-rich, and mixed. 9. Controls using arbitrarily derived triplets with the same compositions, such as reversed codons (25), do not concentrate in amino acid–binding sites.
[Hendry et al., 1981] Otra expresión de la relación estereoquímica entre aminoácidos y nucleótidos es la relación que existe entre los grupos funcionales de los [Mejía, 2016] Todos los aminoácidos afines pueden aminoácidos y lo huecos se crean al remover una base enlazarse al RNA debido a que los grupos α−amino y nitrogenada de la estructura de los ácidos nucleicos 4
4 DNA and RNA have a conical intersec- 7
Information becomes acquired as per-
tion, i.e. they can act as very efficient acceptor quencher molecules to the an-
sistent microscopic dissipative structuring in the form of a genome. All in-
tenna donor molecules like Tryptophan,
formation stored in the genome of any
etc.
organism is ultimately related to the present or extinct dissipation rate of the greater organism to which it belongs, i.e. the biosphere.
5 Other mechanisms to increase dissipation also exist, e.g.
[Rossmann et al., 1974]Establece la conservación de la
making DNA or secuencia gnética con una taza de variación de 1.57 para convertir un aminoácido en otro, la cual resulta mucho
RNA more hydrophobic means that they más baja que una variación aleatoria. También permite will stick to the ocean surface where the establecer y rastrear periodos evolutivos entre especies por ejemplo los simios en los mamiferos. impressed photon potential is greatest. [Yarus et al., 2009] We have tested the idea that the coding triplets arise as essential parts of RNA-like amino acid–binding sites. These ancestral triplets then escape from amino acid–binding sites to acquire new functions as codons and anticodons in a more modern translation apparatus. ——-The process of adding new amino acids to the genetic code in an error-minimizing fashion could, according to modeling, have given the code its overall shape.
Other possible mechanisms are ??.
6 Dissipation-replication mechanism, e.g. UVTAR, associates efficient dissipation with efficient replication (proliferation).
Coevolution____In the description of Wong (9), an initial code, containing a nucleus of codons and primordial, nonbiosynthetic amino acids, is extended to amino acids whose biosynthesis later becomes possible. There has been a lively recent discussion of coevolution initiated by the work of Amirnovin (10), who pointed out that the choice of precursor-product pairs was crucial to the apparent plausibility of coevo- lutionary shaping of the coding table. For example, if pairs from Escherichia coli instead of supposed universal pairs were used, the ability to predict amino acids related by singlebase changes mostly disappeared. Apoyo para trabajar al mismo tiempo con ambos ácidos nucléicos.
This gives the “vitality” to life.
En la secuencia evolutiva de codifcación de aminoácidos es de suponer que los primeros en codificarse fueron los aminoácidos hidrofóbicos, pues está propiedad les permitiria mantenerse en la superficie del agua donde los aminoácidos y los nucleotidos (afines a estos) pueden disipar el potencial fotonico solar.
References [AD et al., 2008] AD, G., Heroux, A., RP, R., and RT, B. (2008). Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem, 283:22347–22351. [Copley et al., 2005] Copley, S. D., Smith, E., and Morowitz, H. J. (2005). A mechanism for the association of amino acids with their codons and the origin of the genetic code. PNAS, 102(12):4442–4447. [Dougherty, 2007] Dougherty, D. A. (2007). Cation-p Interactions Involving Aromatic Amino Acids. The Journal of Nutrition, 137:1504S–1508S.
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[Hendry et al., 1981] Hendry, L. B., Bransome, E. D., Hutson, M. S., and Campbell, L. K. (1981). First approximation of a stereochemical rationale for the genetic code based on the topography and physicochemical properties of “cavities” constructed from models of DNA. Proc. Natl. Acad. Sci. USA, 78(12):7440–7444. [Majerfeld et al., 2005] Majerfeld, I., Puthenvedu, D., and Yarus, M. (2005). Histidine; Genetic Code Origins. J Mol Evol, (61):226–235.
RNA Affinity for Molecular L-
[Majerfeld and Yarus, 2005] Majerfeld, I. and Yarus, M. (2005). A diminutive and specific RNA binding site for L-tryptophan. Nucleic Acids Research, 33(17):5482–5493. [Mejía, 2016] Mejía, J. (2016). Codificación de información en los ácidos nucleicos desde la prespectiva de la teoría termodinámica disipativa del origen de la vida. Master’s thesis, Universidad Nacional Autónoma de México. [Rossmann et al., 1974] Rossmann, M. G., Moras, D., and Olsen, K. W. (1974). Chemical and biological evolution of a nucleotide-biding protein. Nature, 250(5463):194–199. [Serganov et al., 2008] Serganov, A., Huang, L., and DJ, P. (2008). Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature, 455:1263–1267. [Toulmir et al., 1974] Toulmir, J.-J., Charlier, M., and Herliune, C. (1974). Specific Recognition of Single-Stranded Regions in Ultraviolet-Irradiated and Heat-Denatured DNA by Tryptophan-Containing Peptides. Proc. Nat. Acad. Sci., 71(8):3185–3188. [Weber and Lacey, 1978] Weber, A. L. and Lacey, J. (1978). Genetic Code Corelations: Amino Acids and Their Anticodon Nucleotides. J. Mol. Evol., 11:199–210. [Wong, 1975] Wong, J. T. F. (1975). Co-Evolution Theory of Genetic Code. Proceedings of the National Academy of Sciences of the United States of America, 72(5):1909–1912. [Yarus et al., 2009] Yarus, M., Widmann, J., and Knight, R. (2009). RNA-Amino Acid Binding: A Stereochemecal Era for the Genetic Code. J Mol Evol, 69(DOI 10.1007/s00239-009-9270-1):406–429.
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Apéndices Type of Type of Amino acid Codon Affinity Affinity Non-polar with aliphatic R group (hydrophobic) GGU 7.2 GCU 7.8 GGC GCC Ala GGA GCA GGG GCG CCU 5.2 GUU 6.6 CCC GUC Val CCA GUA CCG GUG CUU 9.1 Ile AUU 5.3 CUC AUC CUA AUA CUG AUG 2.3 Group R aromatic (slightly hydrophobic) UUU 3.9 Tyr UAU 3.2 UUC UAC UGG 1.4 Polar R group without charge AGU 6.8 ACU 5.9 AGC ACC Thr AAU 4.3 ACA AAC ACG GGU 4.2 UGU 1.9 Cys GGC UGC GGA GGG Positively charged R group AAA 5.9 CAU 2.3 His AAG CAC CGU 5.1 CGC CGA CGG Group R negatively charged GAU 5.3 GAA 6.3 Glu GAC GAG
Amino acid
Gly
Pro
Leu Met Phe Trp Ser Asn
Gly
Lys
Arg
Asp
Codon
Cuadro 1: Coding of amino acids and the type of affinity that exists with its codon. The amino acids found by S. Miller where Alanin and Glycine. and both of them beloging to the hidrofobic group of amino acids. In the second paper of Yarus and Majerfield they have found an stereochemical affinity between aptamers and his, arg and trp.
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