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The Emergence of Life: From Chemical Origins to Synthetic Biology

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

Deadline for manuscript submissions: closed (30 September 2015) | Viewed by 70395

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Special Issue Editor

Prof. Dr. Pier Luigi Luisi

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Guest Editor

1. Professor emeritus ETH Zurich, Switzerland
2. Dipartimento di Biologia, Università degli Studi di Roma Tre, Viale Marconi 446, 00146 Roma, Italy
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 submissions that pass pre-check are 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 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

prebiotic
origin of life
mininmal cell
synthetic biology
RNA-world

Published Papers (7 papers)

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Research

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974 KiB

Open AccessArticle

Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis

by David S. Ross and David Deamer

Life 2016, 6(3), 28; https://doi.org/10.3390/life6030028 - 26 Jul 2016

Cited by 94 | Viewed by 8052

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 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 N_m + N_n ↔ N_m+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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3071 KiB

Open AccessArticle

Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

by J. Tze-Fei Wong, Siu-Kin Ng, Wai-Kin Mat, Taobo Hu and Hong Xue

Life 2016, 6(1), 12; https://doi.org/10.3390/life6010012 - 16 Mar 2016

Cited by 65 | Viewed by 10439

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 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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1853 KiB

Open AccessReview

Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine

by Rafal Wieczorek, Katarzyna Adamala, Tecla Gasperi, Fabio Polticelli and Pasquale Stano

Life 2017, 7(2), 19; https://doi.org/10.3390/life7020019 - 09 Apr 2017

Cited by 36 | Viewed by 11120

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 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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11493 KiB

Open AccessReview

The Role of Lipid Membranes in Life’s Origin

by David Deamer

Life 2017, 7(1), 5; https://doi.org/10.3390/life7010005 - 17 Jan 2017

Cited by 146 | Viewed by 13058

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 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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2736 KiB

Open AccessReview

Molecular Asymmetry in Prebiotic Chemistry: An Account from Meteorites

by Sandra Pizzarello

Life 2016, 6(2), 18; https://doi.org/10.3390/life6020018 - 13 Apr 2016

Cited by 19 | Viewed by 5397

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 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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1268 KiB

Open AccessReview

Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach)

by Kenji Ikehara

Life 2016, 6(1), 6; https://doi.org/10.3390/life6010006 - 26 Jan 2016

Cited by 18 | Viewed by 15440

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 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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177 KiB

Open AccessReview

On the Origin of Sequence

by Peter T. S. van der Gulik

Life 2015, 5(4), 1629-1637; https://doi.org/10.3390/life5041629 - 16 Nov 2015

Cited by 5 | Viewed by 5554

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 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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