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Phosphorus (P) and the Origins of Life
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Phosphorus (P) and the Origins of Life

A special issue of Life (ISSN 2075-1729).

Deadline for manuscript submissions: closed (30 April 2017) | Viewed by 52832

Special Issue Editor

Dr. Terry Kee

E-Mail Website
Guest Editor
School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
Interests: phosphorus chemistry; abiogenesis; astrobiology

Special Issue Information

Dear Colleagues,

Within the field of abiogenesis, the study of life’s origins, there are many different avenues of exploration which transcend traditional disciplines and attempt to provide both coherent hypotheses and penetrating experimental demonstrations with the aim to shed light on the emergent phenomenon of life. Within such a pan-discipline arena, there are certain recurrent themes which link together work from astronomical, geological, chemical and biological-based teams; one such theme centers on the role of phosphorus in the emergence of life.

Phosphorus has properties, which, to the best of our knowledge, make it uniquely suited to its roles in contemporary biochemistry. The element lies at the heart of all cellular energy currency systems, cell membranes, nucleic acids and metabolism. The mechanisms by which nature first integrated phosphorus into primitive life are not currently known but, as the element holds such importance to extant life processes, it is envisaged that these mechanisms are ancient and fundamental to life’s emergence. Consequently, no model of the emergence of life can be considered complete unless it offers insights into how phosphorus came to occupy the position it does in the chemical process of living.

For these reasons, the investigation of the emergence of phosphorus-based systems in abiogenesis is a significant and rapidly growing field of study. In this Special Issue, some of the most recent discoveries and avenues of investigation are presented; highlighting how far we have come and hinting at how far we have yet to go in understanding this fundamental problem within the field abiogenesis.

Dr. Terry Kee
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • phosphorus chemistry
  • energy currency systems
  • prebiotic
  • geochemistry
  • metabolism
  • protocells
  • nucleic acids

Published Papers (7 papers)

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Research

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3383 KiB  
Article
Effects of Trimetaphosphate on Abiotic Formation and Hydrolysis of Peptides
by Izabela K. Sibilska, Bingming Chen, Lingjun Li and John Yin
Life 2017, 7(4), 50; https://doi.org/10.3390/life7040050 - 30 Nov 2017
Cited by 14 | Viewed by 5706
Abstract
The primordial Earth probably had most of the factors needed for the emergence and development of life. It is believed that it had not only water, but also simple inorganic and organic materials. While studies since the 1950s on the origins of organic [...] Read more.
The primordial Earth probably had most of the factors needed for the emergence and development of life. It is believed that it had not only water, but also simple inorganic and organic materials. While studies since the 1950s on the origins of organic matter have established key roles for amino acids, conditions that would have promoted their condensation to make polymers, such as peptides or proteins, have yet to be fully defined. The condensation of amino acids in a water-rich environment is not thermodynamically favored. Therefore, the efficient formation of peptides requires the presence of a catalyst or the activation of a substrate. In living cells, the biosynthesis of proteins is assisted by enzymes and requires adenosine triphosphate (ATP), a relatively complex organic polyphosphate, which serves as an energy source. Outside the living organism, simpler inorganic polyphosphates can form active aminoacyl–phosphate anhydrides, which suggests the broader potential of phosphorus for enabling the polymerization of amino acids. However, this has yet to be demonstrated. To address this gap, aqueous solutions containing a simple dipeptide, diglycine, and a simple polyphosphate, trimetaphosphate, were dried, and reaction products were analyzed by high performance liquid chromatography and mass spectrometry (HPLC-MS). Different reaction environments, which were defined by the initial solution composition, pH, temperature, and incubation time, were found to affect the distribution and yield of products. Our results collectively provide strong evidence for reactions that both condense and hydrolyze peptides. It is noteworthy that the co-occurrence of reactions that form and cleave peptides are a central feature of Kauffman’s theory for the emergence of autocatalytic sets, which is a key step in the chemical origins of life. Full article
(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)
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3374 KiB  
Article
Chemical Transformations in Proto-Cytoplasmic Media. Phosphorus Coupling in the Silica Hydrogel Phase
by Ian B. Gorrell, Timothy W. Henderson, Kamal Albdeery, Philip M. Savage and Terence P. Kee
Life 2017, 7(4), 45; https://doi.org/10.3390/life7040045 - 19 Nov 2017
Cited by 8 | Viewed by 4772
Abstract
It has been proposed that prebiotic chemical studies on the emergence of primitive life would be most relevant when performed in a hydrogel, rather than an aqueous, environment. In this paper we describe the ambient temperature coupling of phosphorus oxyacids [Pi] mediated by [...] Read more.
It has been proposed that prebiotic chemical studies on the emergence of primitive life would be most relevant when performed in a hydrogel, rather than an aqueous, environment. In this paper we describe the ambient temperature coupling of phosphorus oxyacids [Pi] mediated by Fe(II) under aerobic conditions within a silica hydrogel (SHG) environment. We have chosen to examine SHGs as they have considerable geological precedence as key phases in silicification en route to rock formation. Following a description of the preparation and characterization studies on our SHG formulations, coupling experiments between Pi species are described across multiple permutations of (i) Pi compound; (ii) gel formulation; (iii) metal salt additive; and (iv) pH-modifying agent. The results suggest that successful Pi coupling, indicated by observation of pyrophosphate [PPi(V)] via 31P-NMR spectroscopy, takes place when the following components are present: (i) a mixture of mixture of Pi(III) and Pi(V) or pure PPi(III-V); (ii) Fe(II); (iii) acetic or formic acid (not hydrochloric acid); (iv) aerobic conditions or the presence of H2O2 as an oxidant; and (v) the presence of a gel system. On the basis of these, and aqueous control reactions, we suggest mechanistic possibilities. Full article
(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)
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1105 KiB  
Article
Silicate-Promoted Phosphorylation of Glycerol in Non-Aqueous Solvents: A Prebiotically Plausible Route to Organophosphates
by Maheen Gull, Brian J. Cafferty, Nicholas V. Hud and Matthew A. Pasek
Life 2017, 7(3), 29; https://doi.org/10.3390/life7030029 - 29 Jun 2017
Cited by 22 | Viewed by 6515
Abstract
Phosphorylation reactions of glycerol were studied using different inorganic phosphates such as sodium phosphate, trimetaphosphate (a condensed phosphate), and struvite. The reactions were carried out in two non-aqueous solvents: formamide and a eutectic solvent consisting of choline-chloride and glycerol in a ratio of [...] Read more.
Phosphorylation reactions of glycerol were studied using different inorganic phosphates such as sodium phosphate, trimetaphosphate (a condensed phosphate), and struvite. The reactions were carried out in two non-aqueous solvents: formamide and a eutectic solvent consisting of choline-chloride and glycerol in a ratio of 1:2.5. The glycerol reacted in formamide and in the eutectic solvent with phosphate to yield its phosphorylated derivatives in the presence of silicates such as quartz sand and kaolinite clay. The reactions were carried out by heating glycerol with a phosphate source at 85 °C for one week and were analyzed by 31P-nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). The yield of the phosphorylated glycerol was improved by the presence of silicates, and reached 90% in some experiments. Our findings further support the proposal that non-aqueous solvents are advantageous for the prebiotic synthesis of biomolecules, and suggest that silicates may have aided in the formation of organophosphates on the prebiotic earth. Full article
(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)
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Review

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14310 KiB  
Review
Nitrogenous Derivatives of Phosphorus and the Origins of Life: Plausible Prebiotic Phosphorylating Agents in Water
by Megha Karki, Clémentine Gibard, Subhendu Bhowmik and Ramanarayanan Krishnamurthy
Life 2017, 7(3), 32; https://doi.org/10.3390/life7030032 - 29 Jul 2017
Cited by 40 | Viewed by 11248
Abstract
Phosphorylation under plausible prebiotic conditions continues to be one of the defining issues for the role of phosphorus in the origins of life processes. In this review, we cover the reactions of alternative forms of phosphate, specifically the nitrogenous versions of phosphate (and [...] Read more.
Phosphorylation under plausible prebiotic conditions continues to be one of the defining issues for the role of phosphorus in the origins of life processes. In this review, we cover the reactions of alternative forms of phosphate, specifically the nitrogenous versions of phosphate (and other forms of reduced phosphorus species) from a prebiotic, synthetic organic and biochemistry perspective. The ease with which such amidophosphates or phosphoramidate derivatives phosphorylate a wide variety of substrates suggests that alternative forms of phosphate could have played a role in overcoming the “phosphorylation in water problem”. We submit that serious consideration should be given to the search for primordial sources of nitrogenous versions of phosphate and other versions of phosphorus. Full article
(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)
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3126 KiB  
Review
A Chemist’s Perspective on the Role of Phosphorus at the Origins of Life
by Christian Fernández-García, Adam J. Coggins and Matthew W. Powner
Life 2017, 7(3), 31; https://doi.org/10.3390/life7030031 - 13 Jul 2017
Cited by 49 | Viewed by 10241
Abstract
The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic [...] Read more.
The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic chemistry, and here, we highlight two important aspects of prebiotic phosphate chemistry. Firstly, we discuss prebiotic phosphorylation reactions; we specifically contrast aqueous electrophilic phosphorylation, and aqueous nucleophilic phosphorylation strategies, with dry-state phosphorylations that are mediated by dissociative phosphoryl-transfer. Secondly, we discuss the non-structural roles that phosphates can play in prebiotic chemistry. Here, we focus on the mechanisms by which phosphate has guided prebiotic reactivity through catalysis or buffering effects, to facilitating selective transformations in neutral water. Several prebiotic routes towards the synthesis of nucleotides, amino acids, and core metabolites, that have been facilitated or controlled by phosphate acting as a general acid–base catalyst, pH buffer, or a chemical buffer, are outlined. These facile and subtle mechanisms for incorporation and exploitation of phosphates to orchestrate selective, robust prebiotic chemistry, coupled with the central and universally conserved roles of phosphates in biochemistry, provide an increasingly clear message that understanding phosphate chemistry will be a key element in elucidating the origins of life on Earth. Full article
(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)
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Other

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11 pages, 884 KiB  
Perspective
Potential Role of Inorganic Confined Environments in Prebiotic Phosphorylation
by Avinash Vicholous Dass, Maguy Jaber, André Brack, Frédéric Foucher, Terence P. Kee, Thomas Georgelin and Frances Westall
Life 2018, 8(1), 7; https://doi.org/10.3390/life8010007 - 05 Mar 2018
Cited by 25 | Viewed by 5350
Abstract
A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding [...] Read more.
A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding within confined dimensions is central to the functioning of contemporary biology. There are numerous advantages to confined environments and an attempt to highlight this fact, within this article, has been undertaken, keeping in context the limitations of aqueous phase chemistry in phosphorylation and, to a certain extent, traditional approaches in prebiotic chemistry. Full article
(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)
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575 KiB  
Hypothesis
Has Inositol Played Any Role in the Origin of Life?
by Adolfo Saiardi
Life 2017, 7(2), 24; https://doi.org/10.3390/life7020024 - 05 Jun 2017
Cited by 9 | Viewed by 6739
Abstract
Phosphorus, as phosphate, plays a paramount role in biology. Since phosphate transfer reactions are an integral part of contemporary life, phosphate may have been incorporated into the initial molecules at the very beginning. To facilitate the studies into early phosphate utilization, we should [...] Read more.
Phosphorus, as phosphate, plays a paramount role in biology. Since phosphate transfer reactions are an integral part of contemporary life, phosphate may have been incorporated into the initial molecules at the very beginning. To facilitate the studies into early phosphate utilization, we should look retrospectively to phosphate-rich molecules present in today’s cells. Overlooked by origin of life studies until now, inositol and the inositol phosphates, of which some species possess more phosphate groups that carbon atoms, represent ideal molecules to consider in this context. The current sophisticated association of inositol with phosphate, and the roles that some inositol phosphates play in regulating cellular phosphate homeostasis, intriguingly suggest that inositol might have played some role in the prebiotic process of phosphate exploitation. Inositol can be synthesized abiotically and, unlike glucose or ribose, is chemically stable. This stability makes inositol the ideal candidate for the earliest organophosphate molecules, as primitive inositol phosphates. I also present arguments suggesting roles for some inositol phosphates in early chemical evolution events. Finally, the possible prebiotic synthesis of inositol pyrophosphates could have generated high-energy molecules to be utilized in primitive trans-phosphorylating processes. Full article
(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)
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