Special Issue "The Emergence of Life: From Chemical Origins to Synthetic Biology"

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Chemistry".

Deadline for manuscript submissions: closed (30 September 2015)

Special Issue Editor

Guest Editor
Prof. Dr. Pier Luigi Luisi

1. Professor emeritus ETH Zurich, Switzerland
2. Dipartimento di Biologia, Università degli Studi di Roma Tre, Viale Marconi 446, 00146 Roma, Italy
Website | E-Mail
Phone: 0039065819795
Interests: never born proteins; minimal cell; synthetic biology; emergence of life

Special Issue Information

Dear Colleagues,

The origin of life is still one of the greatest challenges for science. In fact, the Oparin’s pathway that starts from inanimate matter to reach the first self-reproducing cells is a multistep process, and there are open questions, both conceptually and experimentally, at each of these steps. To partly reflect this long pathway, we set up two special issues which will incorporate related papers that reflect a sequence of events leading to the origin of life on the Earth nearly four billion years ago. The present special issue of Life will be devoted to the origin of molecular order and will be organized in four different sections: (a) the biogenesis of the basic building blocks (mononucleotides, amino acids and peptides, membranogenic compounds and lipids); (b) the origin of prebiotic catalysis by organic or inorganic agents; (c) prebiotic synthesis of proteins and nucleic acids, with particular emphasis on the how macromolecular sequential order can emerge; (d) the mutual, causal relation between proteins and nucleic acids, up to the genetic code. The second special issue, “Origin of Cellular Life” (https://www.mdpi.com/journal/life/special_issues/origin_cellular_life) edited by Professor David Deamer, will focus on processes by which organic compounds and products of prebiotic polymerization reactions can undergo self-assembly into encapsulated systems.
The two special issues are now open for submissions. Prospective authors should send a short abstract or tentative title to the Editorial Office at first. If the editors deem the topic to be appropriate for inclusion in one of the special issues, the author will be encouraged to submit a full manuscript.

Prof. Dr. Pier Luigi Luisi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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 quarterly journal published by MDPI.

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Keywords

  • prebiotic
  • origin of life
  • mininmal cell
  • synthetic biology
  • RNA-world

Published Papers (7 papers)

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Research

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Open AccessArticle
Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis
Received: 28 May 2016 / Revised: 30 June 2016 / Accepted: 11 July 2016 / Published: 26 July 2016
Cited by 17 | PDF Full-text (974 KB) | HTML Full-text | XML Full-text
Abstract
The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how [...] Read more.
The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium Nm + Nn ↔ Nm+n + H2O is endoergic by about 3.3 kcal/mol for polynucleotide formation, and the system thus lies far to the left in the starting solutions. Kinetic simulations of the evaporation showed that simple Le Châtelier’s principle shifts were insufficient, but the introduction of oligomer-stabilizing factors of 5–10 kcal/mol both moved the process to the right and respectively boosted and retarded the elongation and hydrolysis rates. Molecular crowding and excluded volume effects in present-day cells yield stabilizing factors of that order, and we argue here that the crowded conditions in the evaporites generate similar effects. Oligomer formation is thus energetically preferred in those settings, but the process is thwarted in each evaporation step as diffusion becomes rate limiting. Rehydration dissipates disordered oligomer clusters in the evaporites, however, and subsequent dry/wet cycling accordingly “ratchets up” the system to an ultimate population of kinetically trappedthermodynamically preferred biopolymers. Full article
(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)
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Open AccessArticle
Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life
Received: 8 January 2016 / Revised: 26 February 2016 / Accepted: 4 March 2016 / Published: 16 March 2016
Cited by 15 | PDF Full-text (3071 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase [...] Read more.
The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets. Full article
(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)
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Review

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Open AccessReview
Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine
Received: 5 February 2017 / Revised: 3 April 2017 / Accepted: 5 April 2017 / Published: 9 April 2017
Cited by 9 | PDF Full-text (1853 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and [...] Read more.
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution. Full article
(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)
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Open AccessReview
The Role of Lipid Membranes in Life’s Origin
Received: 13 December 2016 / Revised: 6 January 2017 / Accepted: 9 January 2017 / Published: 17 January 2017
Cited by 22 | PDF Full-text (11493 KB) | HTML Full-text | XML Full-text
Abstract
At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses [...] Read more.
At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents. Full article
(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)
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Open AccessReview
Molecular Asymmetry in Prebiotic Chemistry: An Account from Meteorites
Received: 8 February 2016 / Revised: 1 April 2016 / Accepted: 7 April 2016 / Published: 13 April 2016
Cited by 4 | PDF Full-text (2736 KB) | HTML Full-text | XML Full-text
Abstract
Carbonaceous Chondrite (CC) meteorites are fragments of asteroids, solar planetesimals that never became large enough to separate matter by their density, like terrestrial planets. CC contains various amounts of organic carbon and carry a record of chemical evolution as it came to be [...] Read more.
Carbonaceous Chondrite (CC) meteorites are fragments of asteroids, solar planetesimals that never became large enough to separate matter by their density, like terrestrial planets. CC contains various amounts of organic carbon and carry a record of chemical evolution as it came to be in the Solar System, at the time the Earth was formed and before the origins of life. We review this record as it pertains to the chiral asymmetry determined for several organic compounds in CC, which reaches a broad molecular distribution and enantiomeric excesses of up to 50%–60%. Because homochirality is an indispensable attribute of extant polymers and these meteoritic enantiomeric excesses are still, to date, the only case of chiral asymmetry in organic molecules measured outside the biosphere, the possibility of an exogenous delivery of primed prebiotic compounds to early Earth from meteorites is often proposed. Whether this exogenous delivery held a chiral advantage in molecular evolution remains an open question, as many others regarding the origins of life are. Full article
(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)
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Open AccessReview
Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach)
Received: 1 November 2015 / Revised: 30 December 2015 / Accepted: 18 January 2016 / Published: 26 January 2016
Cited by 5 | PDF Full-text (1268 KB) | HTML Full-text | XML Full-text
Abstract
It is no doubt quite difficult to solve the riddle of the origin of life. So, firstly, I would like to point out the kinds of obstacles there are in solving this riddle and how we should tackle these difficult problems, reviewing the [...] Read more.
It is no doubt quite difficult to solve the riddle of the origin of life. So, firstly, I would like to point out the kinds of obstacles there are in solving this riddle and how we should tackle these difficult problems, reviewing the studies that have been conducted so far. After that, I will propose that the consecutive evolutionary steps in a timeline can be rationally deduced by using a common event as a juncture, which is obtained by two counter-directional approaches: one is the bottom-up approach through which many researchers have studied the origin of life, and the other is the top-down approach, through which I established the [GADV]-protein world hypothesis or GADV hypothesis on the origin of life starting from a study on the formation of entirely new genes in extant microorganisms. Last, I will describe the probable evolutionary process from the formation of Earth to the emergence of life, which was deduced by using a common event—the establishment of the first genetic code encoding [GADV]-amino acids—as a juncture for the results obtained from the two approaches. Full article
(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)
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Open AccessReview
On the Origin of Sequence
Life 2015, 5(4), 1629-1637; https://doi.org/10.3390/life5041629
Received: 25 September 2015 / Revised: 30 October 2015 / Accepted: 9 November 2015 / Published: 16 November 2015
Cited by 2 | PDF Full-text (177 KB) | HTML Full-text | XML Full-text
Abstract
Three aspects which make planet Earth special, and which must be taken in consideration with respect to the emergence of peptides, are the mineralogical composition, the Moon which is in the same size class, and the triple environment consisting of ocean, atmosphere, and [...] Read more.
Three aspects which make planet Earth special, and which must be taken in consideration with respect to the emergence of peptides, are the mineralogical composition, the Moon which is in the same size class, and the triple environment consisting of ocean, atmosphere, and continent. GlyGly is a remarkable peptide because it stimulates peptide bond formation in the Salt-Induced Peptide Formation reaction. The role glycine and aspartic acid play in the active site of RNA polymerase is remarkable too. GlyGly might have been the original product of coded peptide synthesis because of its importance in stimulating the production of oligopeptides with a high aspartic acid content, which protected small RNA molecules by binding Mg2+ ions. The feedback loop, which is closed by having RNA molecules producing GlyGly, is proposed as the essential element fundamental to life. Having this system running, longer sequences could evolve, gradually solving the problem of error catastrophe. The basic structure of the standard genetic code (8 fourfold degenerate codon boxes and 8 split codon boxes) is an example of the way information concerning the emergence of life is frozen in the biological constitution of organisms: the structure of the code contains historical information. Full article
(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)
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