1
|
Iqubal MA, Sharma R, Kamaluddin, Jheeta S. Synthesis of Nucleic Acid Bases by Metal Ferrite Nanoparticles from a Single Carbon Atom Precursor Molecule: Formamide. ORIGINS LIFE EVOL B 2019; 49:147-162. [PMID: 31444635 DOI: 10.1007/s11084-019-09585-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/09/2019] [Indexed: 10/26/2022]
Abstract
The synthesis of prebiotic molecules from simple precursors is believed to be a crucial scheme in order to study the origin of life processes. The present study describes the one-pot synthesis of purine and pyrimidine nucleic acid bases in the presence of pre-biologically significant binary metal oxide nanoparticles, metal ferrites, namely NiFe2O4, CoFe2O4, CuFe2O4, ZnFe2O4 and MnFe2O4. The products identified are cytosine, isocytosine, 4(3H)-pyrimidinone, adenine, hypoxanthine and purine. The ability of isocytosine (a constitutional isomer of cytosine) to recognize cytosine and guanine through normal and reversed Watson-Crick pairing respectively, demonstrates an important storyline for the genesis of ancient nucleic acids. The relevance of other synthesized nucleic acid bases with respect to the origin of life is also discussed. The divalent metal ions in iron oxide make it an appropriate catalytic system because it demonstrates excellent catalytic performance for the nucleic acid bases synthesis with significantly high yield, as compared to pure iron oxide and some other minerals like silica, alumina, manganese oxides and double metal cyanide complexes.
Collapse
Affiliation(s)
- Mohammad Asif Iqubal
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, UK, 247 667, India.
- Interfield Laboratories, Plot no: C4, Green Industrial Park, Gambheeram Village, Anandapuram Mandal, Visakhapatnam, Andhra Pradesh, 531163, India.
| | - Rachana Sharma
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, UK, 247 667, India
| | - Kamaluddin
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, UK, 247 667, India
| | - Sohan Jheeta
- Network of Researchers on Chemical Evolution of Life, Leeds, LS7 3RB, UK
| |
Collapse
|
2
|
Bhushan B, Nayak A, Kamaluddin. Catalytic Role of Manganese Oxides in Prebiotic Nucleobases Synthesis from Formamide. ORIGINS LIFE EVOL B 2016; 46:203-13. [PMID: 26758444 DOI: 10.1007/s11084-015-9480-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/16/2015] [Indexed: 10/22/2022]
Abstract
Origin of life processes might have begun with the formation of important biomonomers, such as amino acids and nucleotides, from simple molecules present in the prebiotic environment and their subsequent condensation to biopolymers. While studying the prebiotic synthesis of naturally occurring purine and pyrimidine derivatives from formamide, the manganese oxides demonstrated not only good binding for formamide but demonstrated novel catalytic activity. A novel one pot manganese oxide catalyzed synthesis of pyrimidine nucleobases like thymine is reported along with the formation of other nucleobases like purine, 9-(hydroxyacetyl) purine, cytosine, 4(3 H)-pyrimidinone and adenine in acceptable amounts. The work reported is significant in the sense that the synthesis of thymine has exhibited difficulties especially under one pot conditions and also such has been reported only under the catalytic activity of TiO2. The lower oxides of manganese were reported to show higher potential as catalysts and their existence were favored by the reducing atmospheric conditions prevalent on early Earth; thereby confirming the hypothesis that mineral having metals in reduced form might have been more active during the course of chemical evolution. Our results further confirm the role of formamide as a probable precursor for the formation of purine and pyrimidine bases during the course of chemical evolution and origin of life.
Collapse
Affiliation(s)
- Brij Bhushan
- Department of Agrifood Engineering and Biotecnology, Universitat Politècnica de Catalunya (UPC), 08860, Barcelona, Castelldefels, Spain.
| | - Arunima Nayak
- Energy and Environment Department, Innovació i Recerca Industrial i Sostenible, -08860, Castelldefels, Spain
| | - Kamaluddin
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667(U.K.), India
| |
Collapse
|
3
|
Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem Soc Rev 2012; 41:5526-65. [PMID: 22684046 DOI: 10.1039/c2cs35066a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.
Collapse
Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
| | | | | | | | | |
Collapse
|
4
|
Shanker U, Bhushan B, Bhattacharjee G. Formation of nucleobases from formamide in the presence of iron oxides: implication in chemical evolution and origin of life. ASTROBIOLOGY 2011; 11:225-233. [PMID: 21480791 DOI: 10.1089/ast.2010.0530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Simple compounds like HCN, which have one C and one N, are proposed as the probable precursors for biomonomers. Formamide, a hydrolysis product of HCN, is known as the precursor of various biologically important compounds, for example, nucleobases (purines and pyrimidines). In this paper, we report our results on the synthesis of nucleobases, adenine, cytosine, purine, 9-(hydroxyacetyl) purine, and 4(3H)-pyrimidinone from formamide, using iron oxide (hematite) and oxide hydroxides (goethite and akaganeite) as a catalyst. Goethite and hematite produced purine in higher yield. The products formed were characterized by high-performance liquid chromatography and electrospray ionization mass spectrometry techniques. Results of our study reveal that iron oxides might have worked as efficient prebiotic catalysts.
Collapse
Affiliation(s)
- Uma Shanker
- Department of Chemistry, Indian Institute of Technology Roorkee, India
| | | | | |
Collapse
|
5
|
Astrochemistry and the origin of genetic material. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2011. [DOI: 10.1007/s12210-011-0118-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
6
|
Takeuchi N, Hogeweg P. Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization. PLoS Comput Biol 2009; 5:e1000542. [PMID: 19834556 PMCID: PMC2757730 DOI: 10.1371/journal.pcbi.1000542] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 09/21/2009] [Indexed: 11/19/2022] Open
Abstract
Multilevel selection has been indicated as an essential factor for the evolution of complexity in interacting RNA-like replicator systems. There are two types of multilevel selection mechanisms: implicit and explicit. For implicit multilevel selection, spatial self-organization of replicator populations has been suggested, which leads to higher level selection among emergent mesoscopic spatial patterns (traveling waves). For explicit multilevel selection, compartmentalization of replicators by vesicles has been suggested, which leads to higher level evolutionary dynamics among explicitly imposed mesoscopic entities (protocells). Historically, these mechanisms have been given separate consideration for the interests on its own. Here, we make a direct comparison between spatial self-organization and compartmentalization in simulated RNA-like replicator systems. Firstly, we show that both mechanisms achieve the macroscopic stability of a replicator system through the evolutionary dynamics on mesoscopic entities that counteract that of microscopic entities. Secondly, we show that a striking difference exists between the two mechanisms regarding their possible influence on the long-term evolutionary dynamics, which happens under an emergent trade-off situation arising from the multilevel selection. The difference is explained in terms of the difference in the stability between self-organized mesoscopic entities and externally imposed mesoscopic entities. Thirdly, we show that a sharp transition happens in the long-term evolutionary dynamics of the compartmentalized system as a function of replicator mutation rate. Fourthly, the results imply that spatial self-organization can allow the evolution of stable folding in parasitic replicators without any specific functionality in the folding itself. Finally, the results are discussed in relation to the experimental synthesis of chemical Darwinian systems and to the multilevel selection theory of evolutionary biology in general. To conclude, novel evolutionary directions can emerge through interactions between the evolutionary dynamics on multiple levels of organization. Different multilevel selection mechanisms can produce a difference in the long-term evolutionary trend of identical microscopic entities. The origin of life has ever been attracting scientific inquiries. The RNA world hypothesis suggests that, before the evolution of DNA and protein, primordial life was based on RNA-like molecules both for information storage and chemical catalysis. In the simplest form, an RNA world consists of RNA molecules that can catalyze the replication of their own copies. Thus, an interesting question is whether a system of RNA-like replicators can increase its complexity through Darwinian evolution and approach the modern form of life. It is, however, known that simple natural selection acting on individual replicators is insufficient to account for the evolution of complexity due to the evolution of parasite-like templates. Two solutions have been suggested: compartmentalization of replicators by membranes (i.e., protocells) and spatial self-organization of a replicator population. Here, we make a direct comparison of the two suggestions by computer simulations. Our results show that the two suggestions can lead to unanticipated and contrasting consequences in the long-term evolution of replicating molecules. The results also imply a novel advantage in the spatial self-organization for the evolution of complexity in RNA-like replicator systems.
Collapse
Affiliation(s)
- Nobuto Takeuchi
- Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands.
| | | |
Collapse
|
7
|
The Origin of Life: Chemical Evolution of a Metabolic System in a Mineral Honeycomb? J Mol Evol 2009; 69:458-69. [DOI: 10.1007/s00239-009-9278-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
|
8
|
Ciciriello F, Costanzo G, Pino S, Di Mauro E. Spontaneous Generation Revisited at the Molecular Level. Evol Biol 2009. [DOI: 10.1007/978-3-642-00952-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
|
9
|
Takeuchi N, Salazar L, Poole AM, Hogeweg P. The evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription. Biol Direct 2008; 3:33. [PMID: 18694481 PMCID: PMC2648946 DOI: 10.1186/1745-6150-3-33] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 08/11/2008] [Indexed: 11/23/2022] Open
Abstract
Background The simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually become double-stranded and, hence, become unavailable for replication. Thus the problem of how to separate the two strands is considered a major issue for the early evolution of self-replicating RNA. One biologically plausible way to copy a double-stranded RNA is to displace a preexisting strand by a newly synthesized strand. Such copying can in principle be initiated from either the (+) or (-) strand of a double-stranded RNA. Assuming that only one of them, say (+), can act as replicase when single-stranded, strand displacement produces a new replicase if the (-) strand is the template. If, however, the (+) strand is the template, it produces a new template (but no replicase). Modern transcription exhibits extreme strand preference wherein anti-sense strands are always the template. Likewise, replication by strand displacement seems optimal if it also exhibits extreme strand preference wherein (-) strands are always the template, favoring replicase production. Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement. Results We first studied a simple mathematical model of the replicator dynamics. Our results indicated that if the system is well-mixed, there is no selective force acting upon strand preference per se. Next, we studied an individual-based simulation model to investigate the evolution of strand preference under finite diffusion. Interestingly, the results showed that selective forces "emerge" because of finite diffusion. Strikingly, the direction of the strand preference that evolves [i.e. (+) or (-) strand excess] is a complex non-monotonic function of the diffusion intensity. The mechanism underlying this behavior is elucidated. Furthermore, a speciation-like phenomenon is observed under certain conditions: two extreme replication strategies, namely replicase producers and template producers, emerge and coexist among competing replicators. Conclusion Finite diffusion enables the evolution of strand preference, the direction of which is a non-monotonic function of the diffusion intensity. By identifying the conditions under which strand preference evolves, this study provides an insight into how a rudimentary transcription-like pattern might have emerged in an RNA-based replicator system. Reviewers This article was reviewed by Eugene V Koonin, Rob Kinght and István Scheuring (nominated by David H Ardell). For the full reviews, please go to the Reviewers' comments section.
Collapse
Affiliation(s)
- Nobuto Takeuchi
- Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands.
| | | | | | | |
Collapse
|
10
|
Biondi E, Branciamore S, Maurel MC, Gallori E. Montmorillonite protection of an UV-irradiated hairpin ribozyme: evolution of the RNA world in a mineral environment. BMC Evol Biol 2007; 7 Suppl 2:S2. [PMID: 17767730 PMCID: PMC1963481 DOI: 10.1186/1471-2148-7-s2-s2] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background The hypothesis of an RNA-based origin of life, known as the "RNA world", is strongly affected by the hostile environmental conditions probably present in the early Earth. In particular, strong UV and X-ray radiations could have been a major obstacle to the formation and evolution of the first biomolecules. In 1951, J. D. Bernal first proposed that clay minerals could have served as the sites of accumulation and protection from degradation of the first biopolymers, providing the right physical setting for the evolution of more complex systems. Numerous subsequent experimental studies have reinforced this hypothesis. Results The ability of the possibly widespread prebiotic, clay mineral montmorillonite to protect the catalytic RNA molecule ADHR1 (Adenine Dependent Hairpin Ribozyme 1) from UV-induced damages was experimentally checked. In particular, the self-cleavage reaction of the ribozyme was evaluated after UV-irradiation of the molecule in the absence or presence of clay particles. Results obtained showed a three-fold retention of the self-cleavage activity of the montmorillonite-protected molecule, with respect to the same reaction performed by the ribozyme irradiated in the absence of the clay. Conclusion These results provide a suggestion with which RNA, or RNA-like molecules, could have overcame the problem of protection from UV irradiation in the RNA world era, and suggest that a clay-rich environment could have favoured not only the formation of first genetic molecules, but also their evolution towards increasingly complex molecular organization.
Collapse
Affiliation(s)
- Elisa Biondi
- Department of Animal Biology and Genetics, University of Florence, via Romana 17, 50125 – Florence, Italy
| | - Sergio Branciamore
- Department of Animal Biology and Genetics, University of Florence, via Romana 17, 50125 – Florence, Italy
| | - Marie-Christine Maurel
- Institut Jacques Monod, Laboratoire de Biochimie de l'Evolution et Adaptabilité Moléculaire, Université Paris VI, Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France
| | - Enzo Gallori
- Department of Animal Biology and Genetics, University of Florence, via Romana 17, 50125 – Florence, Italy
| |
Collapse
|