A hypothesis about the origin of biology

Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria

The growth and survival of an organism in a particular environment is highly depends on the certain indispensable genes, termed as essential genes. Sulfate-reducing bacteria (SRB) are obligate anaerobes which thrives on sulfate reduction for its energy requirements. The present study used Oleidesulfovibrio alaskensis G20 (OA G20) as a model SRB to categorize the essential genes based on their key metabolic pathways. Herein, we reported a feedback loop framework for gene of interest discovery, from bio-problem to gene set of interest, leveraging expert annotation with computational prediction. Defined bio-problem was applied to retrieve the genes of SRB from literature databases (PubMed, and PubMed Central) and annotated them to the genome of OA G20. Retrieved gene list was further used to enrich protein-protein interaction and was corroborated to the pangenome analysis, to categorize the enriched gene sets and the respective pathways under essential and non-essential. Interestingly, the sat gene (dde_2265) from the sulfur metabolism was the bridging gene between all the enriched pathways. Gene clusters involved in essential pathways were linked with the genes from seleno-compound metabolism, amino acid metabolism, secondary metabolite synthesis, and cofactor biosynthesis. Furthermore, pangenome analysis demonstrated the gene distribution, where 69.83% of the 116 enriched genes were mapped under "persistent," inferring the essentiality of these genes. Likewise, 21.55% of the enriched genes, which involves specially the formate dehydrogenases and metallic hydrogenases, appeared under "shell." Our methodology suggested that semi-automated text mining and network analysis may play a crucial role in deciphering the previously unexplored genes and key mechanisms which can help to generate a baseline prior to perform any experimental studies.

Thermodynamic Analysis of the Landolt-Type Autocatalytic System

A recent work demonstrated the example of the Landolt-type reaction system and how the simplest autocatalytic loop is described by the kinetic mass action law and proper parametrization of direct and autocatalytic pathways. Using a methodology of non-equilibrium thermodynamics, the thermodynamic consistency of that kinetic model is analyzed and the mass action description is generalized, including an alternative description by the empirical rate equation. Relationships between independent and dependent reactions and their rates are given. The mathematical modeling shows that following the time evolution of reaction rates provides additional insight into autocatalytic behavior. A brief note on thermodynamic driving forces and coupling with diffusion is added. In summary, this work extends and generalizes the kinetic description of the Landolt-type system, placing it within the framework of non-equilibrium thermodynamics and demonstrating its thermodynamic consistency.

Molecular shape as a key source of prebiotic information

One of the most striking features of a living system is the self-sustaining functional inner organization, which is only possible when a source of internal references is available from which the system is able to self-organize components and processes. Internal references are intrinsically related to biological information, which is typically understood as genetic information. However, the organization in living systems supports a diversity of intricate processes that enable life to endure, adapt and reproduce because of this organization. In a biological context, information refers to a complex relationship between internal architecture and system functionality. Nongenetic processes, such as conformational recognition, are not considered biological information, although they exert important control over cell processes. In this contribution, we discuss the informational nature in the recognition of molecular shape in living systems. Thus, we highlight supramolecular matching as having a theoretical key role in the origin of life. Based on recent data, we demonstrate that the transfer of molecular conformation is a very likely dynamic of prebiotic information, which is closely related to the origin of biological homochirality and biogenic systems. In light of the current hypothesis, we also revisit the central dogma of molecular biology to assess the consistency of the proposal presented here. We conclude that both spatial (molecular shape) and sequential (genetic) information must be represented in this biological paradigm.

In search of a primitive signaling code

Cells must have preceded by simpler chemical systems (protocells) that had the capacity of a spontaneous self-assembly process and the ability to confine chemical reaction networks together with a form of information. The presence of lipid molecules in the early Earth conditions is sufficient to ensure the occurrence of spontaneous self-assembly processes, not defined by genetic information, but related to their chemical amphiphilic nature. Ribozymes are plausible molecules for early life, being the first small polynucleotides made up of random oligomers or formed by non-enzymatic template copying. Compartmentalization represents a strategy for the evolution of ribozymes; the attachment of ribozymes to surfaces, such as formed by lipid micellar aggregates may be particular relevant if the surface itself catalyzes RNA polymerization.It is conceivable that the transition from pre-biotic molecular aggregates to cellular life required the coevolution of the RNA world, capable of synthesizing specific, instead of statistical proteins, and of the Lipid world, with a transition from micellar aggregates to semipermeable vesicles. Small molecules available in the prebiotic inventory might promote RNA stability and the evolution of hydrophobic micellar aggregates into membrane-delimited vesicles. The transition from ribozymes catalyzing the assembly of statistical polypeptides to the synthesis of proteins, required the appearance of the genetic code; the transition from hydrophobic platforms favoring the stability of ribozymes and of nascent polypeptides to the selective transport of reagents through a membrane, required the appearance of the signal transduction code.A further integration between the RNA and Lipid worlds can be advanced, taking into account the emerging roles of phospholipid aggregates not only in ensuring stability to ribozymes by compartmentalization, but also in a crucial step of evolution through natural selection mechanisms, based on signal transduction pathways that convert environmental changes into biochemical responses that could vary according to the context. Here I present evidences on the presence of traces of the evolution of a signal transduction system in extant cells, which utilize a phosphoinositide signaling system located both at nucleoplasmic level as well as at the plasma membrane, based on the very same molecules but responding to different rules. The model herewith proposed is based on the following assumptions on the biomolecules of extant organisms: i) amphiphils can be converted into structured aggregates by hydrophobic forces thus giving rise to functional platforms for the interaction of other biomolecules and to their compartmentalization; ii) fundamental biochemical pathways, including protein synthesis, can be sustained by natural ribozymes of ancient origin; iii) ribozymes and nucleotide-derived coenzymes could have existed long before protein enzymes emerged; iv) signaling molecules, both derived from phospholipids and from RNAs could have guided the evolution of complex metabolic processes before the emergence of proteins.

Is pre-Darwinian evolution plausible?

Background

This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin of the first systems capable of Darwinian evolution. The researchers’ responses to eight crucial questions are reviewed. The majority of the researchers claim that there would have been an evolutionary continuity between chemistry and “biology”. A key question is how did this evolution begin before Darwinian evolution had begun? In other words the question is whether pre-Darwinian evolution is plausible.

Results

Strengths and weaknesses of the reviewed scenarios are presented. They are distinguished between metabolism-first, replicator-first and combined metabolism-replicator models. The metabolism-first scenarios show major issues, the worst concerns heredity and chirality. Although the replicator-first scenarios answer the heredity question they have their own problems, notably chirality. Among the reviewed combined metabolism-replicator models, one shows the fewest issues. In particular, it seems to answer the chiral question, and eventually implies Darwinian evolution from the very beginning. Its main hypothesis needs to be validated with experimental data.

Conclusion

From this critical review it is that the concept of “pre-Darwinian evolution” appears questionable, in particular because it is unlikely if not impossible that any evolution in complexity over time may work without multiplication and heritability allowing the emergence of genetically and ecologically diverse lineages on which natural selection may operate. Only Darwinian evolution could have led to such an evolution. Thus, Pre-Darwinian evolution is not plausible according to the author. Surely, the answer to the question posed in the title is a prerequisite to the understanding of the origin of Darwinian evolution.

Reviewers

This article was reviewed by Purificacion Lopez-Garcia, Anthony Poole, Doron Lancet, and Thomas Dandekar.

Research program for a search of the origin of Darwinian evolution : Research program for a vesicle-based model of the origin of Darwinian evolution on prebiotic early Earth

The search for origin of 'life' is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian evolution (Cleland and Chyba 2002). Within a physical approach which has been defined as a level-4 evolution (Tessera and Hoelzer 2013), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.

A Self-Assembled Aggregate Composed of a Fatty Acid Membrane and the Building Blocks of Biological Polymers Provides a First Step in the Emergence of Protocells

We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then explain how the conformational constraints and altered chemical environment due to binding of the components to the membrane could facilitate the formation of nucleosides, oligonucleotides and peptides. We conclude by discussing how the resulting oligomers, even if short and random, could have increased vesicle stability and growth more than their building blocks did, and how competition among these vesicles could have led to longer polymers with complex functions.

Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection

Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.