Special Issue "Systems Protobiology: Origin of Life by Mutually Catalytic Networks"

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

Deadline for manuscript submissions: closed (31 July 2019).

Special Issue Editor

Prof. Doron Lancet
Website
Guest Editor
Department Molecular Genetics Weizmann Institute of Science, Herzl 234, Rehovot 7610010, Israel
Interests: Systems Biology; Systems Prebiology; Mutually Catalytic Networks; Genome; Origin of Life

Special Issue Information

Dear Colleagues,

NASA’s definition of minimal life asserts that “Life is a self-sustaining chemical system capable of Darwinian evolution”. A majority opinion contends that self-sustaining and replicating capacities can only be attained via templating biopolymers such as RNA, which copy sequence information. An alternative upcoming approach claims that life began with mutually-catalytic networks, endowed with self-sustaining and reproduction capabilities, i.e. capable of reproducing their network structure and composition. The first school (“RNA first”) asserts that RNA is necessary even for a most rudimentary evolutionary process. The second (identified with “metabolism first”) claims that, under some circumstances, metabolism-like networks can evolve, and that RNA likely emerged as a product of lengthy evolution. RNA first implies that a single type of molecule with high internal complexity could jump-start life, later recruiting metabolism and enclosure. Metabolism first takes the stand that life was a multi-component network of diverse interacting molecules right from the beginning. In published research it is shown that such networks constitute not only catalysis-based metabolism, but also assume compartment and replication traits. This scenario is obviously much more life-like, and is analyzable by tools of the newly emerging disciplines of Systems Biology and Systems Chemistry.

A cornerstone of the proposed special issue is “Systems Protobiology”, indicating a merger between Systems Sciences and research that strives to define and understand early protocellular life forms. As such, papers in this Special Issue are expected to maintain standards of Systems Sciences, including rigorous chemical definitions, kinetic formalisms and adherence to irreversible thermodynamics directives, as befits a life-like dynamic network away from equilibrium. One of the main goals of Systems Protobiology is demonstrating replication/reproduction and evolvability that does not necessarily depend on long informational polymers. We encourage exploring the notion that RNA and proteins are products of evolution, implying that understanding the abiogenesis of RNA is less critical. Delineating bottom-up paths to life-like processes such as non-enzymatic catalysis, photosynthesis, the emergence of high-energy compounds, as well as membrane generation, dynamics and transport, appear highly relevant. So is the emergence of life-like oligomers of any kind, with templating being one of many ways for network molecules to interact with each other. Experimental approaches addressing mutually catalytic networks are invited, as are pertinent computer analyses and simulations, including the potential role of powerful future computing in deciphering life’s origin.


Prof. Doron Lancet
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 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 1400 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

  • mutually catalytic networks
  • autocatalytic sets
  • protometabolism
  • functional membranes
  • kinetic analyses
  • thermodynamics
  • away from equilibrium
  • replication/reproduction
  • evolvability
  • computer simulations

Published Papers (5 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle
Chemical Ecosystem Selection on Mineral Surfaces Reveals Long-Term Dynamics Consistent with the Spontaneous Emergence of Mutual Catalysis
Life 2019, 9(4), 80; https://doi.org/10.3390/life9040080 - 23 Oct 2019
Cited by 6
Abstract
How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the first evolvers were chemical ecosystems localized on mineral surfaces and composed of sets of molecular species that could catalyze each other’s formation. We used [...] Read more.
How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the first evolvers were chemical ecosystems localized on mineral surfaces and composed of sets of molecular species that could catalyze each other’s formation. We used a bottom-up experimental framework, chemical ecosystem selection (CES), to evaluate this perspective and search for surface-associated and mutually catalytic chemical systems based on the changes in chemistry that they are expected to induce. Here, we report the results of preliminary CES experiments conducted using a synthetic “prebiotic soup” and pyrite grains, which yielded dynamical patterns that are suggestive of the emergence of mutual catalysis. While more research is needed to better understand the specific patterns observed here and determine whether they are reflective of self-propagation, these results illustrate the potential power of CES to test competing hypotheses for the emergence of protobiological chemical systems. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
Show Figures

Figure 1

Open AccessFeature PaperArticle
Molecular Diversity and Network Complexity in Growing Protocells
Life 2019, 9(2), 53; https://doi.org/10.3390/life9020053 - 20 Jun 2019
Abstract
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address the essential role of the huge diversity of cellular components, we studied a model of protocells that convert resources into catalysts with [...] Read more.
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address the essential role of the huge diversity of cellular components, we studied a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources were limited, the diversity in the intracellular components was found to be increased to allow the use of diverse resources for cellular growth. A scaling relation was demonstrated between resource abundances and molecular diversity. In the present study, we examined how the molecular species diversify and how complex catalytic reaction networks develop through an evolutionary course. At some generations, molecular species first appear as parasites that do not contribute to the replication of other molecules. Later, the species turn into host species that contribute to the replication of other species, with further diversification of molecular species. Thus, a complex joint network evolves with this successive increase in species. The present study sheds new light on the origin of molecular diversity and complex reaction networks at the primitive stage of a cell. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
Show Figures

Figure 1

Open AccessArticle
Emergence of a “Cyclosome” in a Primitive Network Capable of Building “Infinite” Proteins
Life 2019, 9(2), 51; https://doi.org/10.3390/life9020051 - 18 Jun 2019
Cited by 12
Abstract
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These [...] Read more.
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included “infinite” proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon’s synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
Show Figures

Figure 1

Open AccessArticle
Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World
Life 2018, 8(3), 33; https://doi.org/10.3390/life8030033 - 18 Aug 2018
Cited by 6
Abstract
Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different [...] Read more.
Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different combinations within compartments, i.e., so-called protocells. However, these previous studies have so far not explicitly modeled the emergence and dynamics of autocatalytic sets in populations of compartments in a spatial environment. Here, we use a recently developed software tool to simulate exactly this scenario, as an important first step towards more realistic simulations and experiments on autocatalytic sets in protocells. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
Show Figures

Graphical abstract

Review

Jump to: Research

Open AccessReview
Autocatalytic Networks at the Basis of Life’s Origin and Organization
Life 2018, 8(4), 62; https://doi.org/10.3390/life8040062 - 08 Dec 2018
Cited by 8
Abstract
Life is more than the sum of its constituent molecules. Living systems depend on a particular chemical organization, i.e., the ways in which their constituent molecules interact and cooperate with each other through catalyzed chemical reactions. Several abstract models of minimal life, based [...] Read more.
Life is more than the sum of its constituent molecules. Living systems depend on a particular chemical organization, i.e., the ways in which their constituent molecules interact and cooperate with each other through catalyzed chemical reactions. Several abstract models of minimal life, based on this idea of chemical organization and also in the context of the origin of life, were developed independently in the 1960s and 1970s. These models include hypercycles, chemotons, autopoietic systems, (M,R)-systems, and autocatalytic sets. We briefly compare these various models, and then focus more specifically on the concept of autocatalytic sets and their mathematical formalization, RAF theory. We argue that autocatalytic sets are a necessary (although not sufficient) condition for life-like behavior. We then elaborate on the suggestion that simple inorganic molecules like metals and minerals may have been the earliest catalysts in the formation of prebiotic autocatalytic sets, and how RAF theory may also be applied to systems beyond chemistry, such as ecology, economics, and cognition. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
Show Figures

Figure 1

Back to TopTop