The self-referential genetic code becoming experimental for synthetic biology
Lab Biodiversidade e Evolucao Molecular, Brazil
Formation of the code follows proteins binding to and stabilizing activities of proto-tRNAs. Mini-tRNAs are proto-tRNA mimics: helices of the acceptor arms and loops that acquire the anticodon function along the process of dimer-directed protein synthesis. Proteins start aperiodic, RNA-binding, N-end stabilized, gradually hydropathy correlated and based on C1 unit metabolism with Acetyl-CoA then the Gly-Ser pathway. Dimer-directed protein synthesis could evolve under a variety of contexts.
A Discontinuous Protocellular Life Scenario in a Porous Mineral Matrix
Delft University of Technology, The Netherlands
I propose that early cellular life might have consisted in a population of short-lived liposomes embedded in a porous inorganic environment with microcavities and tunnels, which assists the coordinated development of a protocytoplasm and the protocell membrane through repetitive disruption and reformation of liposomes up to the higher level of complexity required for permanent cellularization and genetic control.
Reconstructing the Enzymatic and Metabolic Capabilities of Early Lifeforms Through Bioinformatic Metaconsensus
1Princeton University, USA; 2University of Washington, USA
We identify consensus between universal features of genome sequences, protein structures, and metabolic networks to predict a suite of ancient enzyme functions. Using these enzyme functions, we infer metabolic properties of lifeforms at the later stages of the origin of life. We find that this limited catalytic regimen can form a surprisingly complex metabolic network that spans most of modern core metabolism.
Early determinants of the genetic code
IST Austria, Austria
The early coevolution of the genetic code and the synthetases (proteins that charge tRNAs with amino acids) is studied. Two families of synthetases exist, having different modes of recognizing tRNA stems. However, they can confuse some tRNAs, incorrectly charging them. Studying the kinetics of this reaction shows that the current mode is maladaptive. The evolution of protocells bearing distinct modes explains the diversification and specialization of the synthetases in targeting cognate tRNAs.
The physical basis for the early evolution of cell membranes
Massachusetts General Hospital, United States of America
We show how surprisingly low levels of phospholipids can drive protocell membrane growth during competition for single-chain lipids. The ability to synthesize phospholipids would have therefore been highly advantageous for early cells featuring primitive, single-chain membranes. We propose that this transition to phospholipid cell membranes would have led to new selective pressures for the evolution of metabolic and transport machinery to overcome an intrinsic reduction in membrane permeability.
Ice as a medium for RNA replication
MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
Due to RNA’s susceptibility to degradation, an "RNA world" could only have emerged in an environment capable of both protecting RNA integrity and supporting RNA replication and evolution. We have shown that ice, a simple medium widespread in the solar system and, presumably, planetary bodies in general, could have provided such an environment. Ice stabilizes RNA and enhances its ability to replicate and evolve by concentration and confinement in the intricate network of the ice eutectic phase.
Significance of Protein 0th-order Structure for the Origin of Life
1The Open University of Japan, Japan; 2International Institute for Advanced Studies of Japan; 3Narasaho College, Japan
RNA world and GADV hypotheses have been proposed for explanation of the origin of life on the primitive earth. But, the most important point for solving the riddle on the origin of life must be to explain the formation processes of genes, genetic code and proteins. Those processes are rationally explained by the GADV hypothesis. In addition, it makes the GADV hypothesis plausible that [GADV]-proteins could acquire versatile catalytic activities at a high probability.
LUCA (Last Universal Common Ancestor): A cross-platform, open-source software coding model
Microbes-Mind Forum, NASA Ames Research Center, United States of America
Intelligent systems modeled on life are informed by parallels between LUCA (our Last Universal Common Ancestor) and distributed knowledge networks. Hypothesis formation about origins sheds light on problem-solving methods. The A-PR Hypothesis (Autonomy and Pattern Recognition) characterizes how a web-like view of LUCA, as life’s original, open source, cross-platform software coding experiment can inform our efforts to create future systems manifesting collaborative intelligence.
New evidence of early life found in >3.74 Ga meta-sedimentary rocks of Isua Supracrustal Belt, Greenland
Tohoku University, Japan
New graphite-rich schist layers were found in the 3.8 Ga Isua Supracrustal Belt. Carbon isotope compositions of the graphite range from -22 to -16 per mil with an average of -19 per mil. High-resolution transmission electron microscope images of the 13C-depleted graphite show onion-like structures on the nano-scale. Such texture is analogous to previously reported pyrolysed and pressurised biogenic molecules. These results, combined with geological observations, allow us to claim new evidence of early life.
Adsorption of DNA on Fe-Mg rich phyllosilicates characteristics of early oceanic environments
1Laboratoire de Géologie de Lyon : Terre Planètes Environnement, ENS de Lyon, Université Lyon 1, UMR 5276; 2Institut de Génomique Fonctionnelle de Lyon, Université Lyon 1, UMR 5242, INRA, ENS de Lyon; 3Laboratoire Environnement et Minéralurgie, Institut National Polytechnique de Lorraine, UMR 7569
We investigated the adsorption of mononucleotides on mineral surfaces. Montmorillonite has indeed been extensively studied, but other phyllosilicates such as nontronite, although highly probable on the Hadean/Archean ocean floor, have until now been ignored. We used UV absorbance at 260 nm to monitor the adsorption of guanosine and cytidine to several phyllosilicates surfaces, X-ray diffraction and vibrational spectroscopy to characterize the modalities of adsorption.
What can we learn from GFAJ-1 for defining life?
University of Vienna, Research Platform: ExoLife/Institute for Astronomy, Vienna, Austria
With the discovery of the ability of GFAJ-1 to use arsenate instead of phosphate for its biochemical mechanisms the theory of exotic life experienced a boost. We will discuss how the discovery of GFAJ-1 will influence our present strategy for the search for life. The “follow-the-water”-strategy can and should still be used for a first rough determination of habitable planets and moons, but only a “follow-the-nutrients”-strategy will allow to learn more about potential life in these habitats.
Interpretation in Proto-biotic Systems: proposal for a minimal molecular semiotic entity
1University of Exeter, United Kingdom; 2Portland State University, Or., USA
We have published a definition of interpretation, which we take to be a defining property of living things. We show that a single ribozyme could meet our definition. We report artificial evolution of a modified DSL ligase ribozyme, and computer modelling of a ligase catalysing its own synthesis. Results identify a truly minimal case of protobiotically-relevant interpretation. Interpretation constitutes an important and underexplored diagnostic in the evaluation of possible proto-biotic systems.
High Self-Catalysis Leads to Evolutionary ‘Dead-End’
Weizmann Institute of Science, Israel
A key question in the origins of life is how the balance between self and mutual catalysis shapes the behavior of model evolving systems. In this study, we have analyzed the amount of self- and mutual- catalysis in GARD (autocatalytic replication domain) networks, to find that a specific range of self-catalysis level in a network is required to allow high diversity and evolvability, and non-neutral selection of the compositional assemblies.
Lipid biomarker profiles of microbial mats and stromatolites from Hamelin Pool, Shark Bay, Western Australia
1School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; 2Australian Centre for Astrobiology, Sydney, Australia; 3Space Science Division, NASA Ames Research Center, Moffett Field, USA; 4NASA Astrobiology Institute, Moffett Field, USA; 5Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, USA
We examined hydrocarbons, alkyl(wax)-esters, sterols, fatty acids, triterpenoids and ether-linked hydrocarbons from extant intertidal columnar stromatolites and non-lithified smooth and pustular microbial mats from Hamelin Pool. Biomarkers for cyanobacteria, heterotrophic bacteria, sulfate-reducing bacteria, anoxygenic phototrophic bacteria and archaea were present. Though these benthic communities differed in microbial composition and lithification status, their lipid profiles were similar.
Lipid membranes in the cenancestor: did they exist and how were they?
Université Paris Sud 11, France
Dramatic differences in the composition of contemporary membranes in the three domains of life have raised hot controversies between authors thinking that lipid membranes emerged twice independently in evolution and those defending that contemporary membranes diverged from a lipid membrane already present in the last common ancestor of all organisms (cenancestor). We report strong phylogenomic arguments supporting the latter hypothesis and discuss the nature of the membrane of the cenancestor.
Microbial mats from alkaline hot springs in Barguzin basin (Baikal Rift Zone) as a model for studying early ecosystem and mineral formation
1Institute of Geology and Mineralogy SB RAS, Russia; 2Boreskov Institute of Catalysis SB RAS, Russia; 3Institute of Cytology and Genetics SB RAS, Russia
The geochemical, microbiological and physical-chemical methods were used to study of hot springs of the Baikal Rift Zone. Te carbonate agglomerates are only formed at three sites. The largest carbonate body is formed on the Garga spring. The structure of this body as well as the structure of cyanobacterial community was studied. The conclusion that the carbonate body was formed as a result both of the deposition of minerals from the hot spring stream and of cyanobacterial community activities was made.
Evolutionary history of ATP-synthases provides clues for the origin and early function of membranes and membrane proteins
Laboratory of Molecular Plant Biology, University of Turku, Finland
Precursors of the ubiquitously conserved subunits of ATP-synthases probably included an RNA helicase and a Na+ channel, which we suggest could have been factors in primitive RNA replication complexes located in internal membrane layers of early molecular communities. In such locations, they would not have served to pump ions through the membrane, but rather – akin to modern +RNA viruses – to transport RNA into transient replication vesicles, eventually giving rise to the first protocells.
The Role of Paralogous Duplications in Early Protein Evolution
1Origin of Life Laboratory, Science Faculty, UNAM, Mexico; 2Department of Evolutionary Biology, University of Florence, Firenze, Italy
Clues of the genetic organization and biochemical complexity of primitive entities from which the LCA evolved may be derived from the analysis of next paralogous gene families:
– gene families which have undergone multiple paralogous duplications;
– families formed by a small number of paralogous sequences; and
– sequences formed by duplications followed by gene fusion events.
The significance of these three difference groups to our understanding of early biological evolution will be discussed.
Evolution of Lipid Metabolism in Archaea
Laboratorio de Origen de la Vida, Facultad de Ciencias, Univ, Mexico
There is little information regarding the role and evolution of lipids molecules that are not part of the archaeal membrane; these include their role as signal molecules, energy storage, among others. Here we report preliminary advances in the development of a detailed overview of archaeas lipid metabolism based on genome sequences analysis. Various pathways with potential metabolic activity have been tentatively identified.
The iron-sulfur autotrophic theory of the origin of life: a critical assessment based on transition metal binding signatures in protein components of the translation machinery
1Laboratorio de Origen de la Vida, Facultad de Ciencias, UNAM, Mexico; 2Institut Cavanilles de Biodiversitat i Biología Evolutiva, Universitat de València, València, SPAIN; 3Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0212, USA
We critically examine the proposal by G. Wächsterhäuser that putative transition metal binding sites in protein components of the translation machinery of hyperthermophiles provide evidence of a direct relationship with the FeS clusters of pyrite and other mineral sulfides and indicate an autotrophic origin of life in volcanic environments. Bioinformatic analysis of the protein components of the translation machinery from several organisms does not support the suggestion made by Wächsterhäuser.
Determination of the gene complement of the last common ancestor: a critical comparison of different bioinformatic methodologies
Facultad de Ciencias, UNAM, Mexico
The last common ancestor (LCA) was an entity similar to extant prokaryotes, the different attempts to reconstruct and characterize its nature are still debated. Comparative genomics analyses can lead to a characterization of the gene complement of the LCA. In this work we present the results of a comparative analyses of the different methodologies that have been developed to characterize the LCA and discuss their underlying premises in an attempt to understand their different results
Arsenic as an electron acceptor for bacterial metabolism, as an example of bacterial adaptation
1Department of Environmental Sciences, University of Siena, Italy; 2Department of Chemistry, University of Siena, Italy
Bacteria in early life could have used different elements to produce energy. An anaerobic bacterial strain was isolated from the deeper polluted sediments, showing the ability to respire As(V) and sulphate, (SO42-), using lactate as an electron donor, with production of a yellow precipitate. Scanning and transmission electron microscopy highlighted precipitates on and inside bacterial cells. A bacterial adaptation to As(V) was evidenced, as an use of elements by bacteria for metabolism.
Colonies of giant vesicles as models of primitive cell communities.
Roma 3 university, Italy
Giant Vesicles (GVs) are used to model individual early cells as well as communities of cells. GVs have been produced by droplet transfer, encapsulating high amount of water-soluble solutes. Models of primitive colonies have been created and characterized by exploiting the electrostatic attraction among vesicles and charged polypeptides. GVs colonies have the advantages of being stable against convective flow and osmotic stress, and exchange solutes, favouring the onset of early cell reactions.
A stepwise, modular evolution-based model for the origin of the RNA World
Department of Molecular Evolution, Centro de Astrobiologia, Spain
We present a stepwise model of ligation-based, modular evolution of RNA that could have bridged the gap between the first RNA oligomers, obtained by random polymerization of ribonucleotides, and a template-dependent RNA polymerase ribozyme. Our evolutionary model, based on computational analyses of the sequence-structure-function relationships in evolving RNA molecules, shows two main advantages with respect to previous hypotheses put forward for the origin of the RNA world.
Simultaneous Cognitive Origin of Life and Information : Origin of Life as a ‘‘Minimum Cognitive System’’
1Faculty of Science, Niigata University, Japan; 2Narasaho College, Japan
Shannon’s information quantity, I(E) = log (1/P(E)), is defined under the existence of “cognitive subjective entity” capable of judging occurred/non-occurred of an event E. Final acceptor/user of information is a living individual, and information-cognizing/-using faculty is a most essential character of living individuals. Information and life emerged simultaneously as “minimum cognitive system”. Bioindividuals are self-revising cognitive leaning machines of neural network type.
A role for genome plasticity in the evolution and cold adaptation of the psychrophilic archaeon Methanococcoides burtonii
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
Comparative genome analysis revealed a wide variety of cold-associated features in the M. burtonii genome including cold-shock proteins, chaperones, RNA helicases, tRNA modification systems, and sensitive signal transduction systems. Alongside these features, genome plasticity (via nucleotide skew, transposon activity and horizontal gene transfer) appears to be of central importance in M. burtonii’s adaptation to the extreme cold of its Antarctic lake environment.
Proton Pumping: Life's Energy Machine from Prebiotic Times to Today.
Rockefeller University, United States of America
“Proto-life” must have had a reliable mechanism to convert energy to order, consistent with near-to-equilibrium thermodynamics Prigogine (NET) a) a steady narrow-range energy supply, b) orderly repetitive motion, c) each step near to equilibrium, d) return to orderly motion when disrupted. I propose that proton pumping across membranes was both the original and continuing NET mechanism in living cells. Consistent with NET, proton-pumping proteins expand and compact with each proton discharged.
Product inhibition-free autocatalysis leads to competition between self-assembling replicators emerging from a dynamic combinatorial library
1Centre for Systems Chemistry, Stratingh Institute, University of Groningen, The Netherlands; 2Department of Chemistry, University of Cambridge, UK; 3Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
We present a dynamic combinatorial library of thiol-functionalized oligopeptide derivatives, which cyclic oligomers are capable of competitive autocatalytic self-assembly into fibrous nanostructures. Operating the system in open flow conditions can provide interesting further insights into the dynamic kinetic stability of these replicators. Their freedom from product inhibition makes this replicating system even more interesting from an origins of life perspective.
An experimental study on the ‘lipid divide’: phase behavior of mixtures of n-acyl and polyprenyl lipids
1Unidad de Biofísica (CSIC-UPV/EHU) Universidad del País Vasco, Spain; 2Dpto. Lógica y Filosofía de la Ciencia, UPV/EHU, Spain
Archaeal and bacterial/eukaryotic membrane lipids differ in stereochemistry and hydrocarbon chain structure. We used confocal microscopy in GUVs and DSC to study the phase behavior of mixtures of DiePC (an isoprenoid lipid) and DPPC (a fatty acid lipid). Domains were visualized in the system DiePC:DPPC (1:1). The phase behavior of mixtures of these types of lipids is being explored because it could also be important to understand the segregation that lead to the ancestors of Archaea and Bacteria
Can a cooperative network of RNA replicators meet criteria for a hypercycle?
1Portland State University, Portland OR, USA; 2Harvard University, Cambridge MA, USA; 3University of Zürich, Switzerland
Eigen developed the notion of the hypercycle, a catalytic set of interdependent cycles, in the 1970's to explain how nascent life may have persisted despite the possibility of information decay through an error catastrophe. But a real-life example of a hypercycle has never been demonstrated with nucleic acids. Here we construct a putative hypercycle entirely from self-assembling and self-replicating RNA fragments and test their ability to behave as Eigen predicted.
Formation of Intermolecular RNA Complexes in Frozen Solution
1School of Biology Georgia Institute of Technology, United States of America; 2NASA Astrobiology Institute and the Center for Ribosomal Origins and Evolution at the Georgia Institute of Technology.
Freezing dilute solutions of short RNA hairpin oligomers (15-21 nt) with Tm’s > 80 oC results in meta-stable intermolecular complexes. The influence of temperature, ionic environment, RNA sequence and concentration indicate that assembly is thermodynamically driven by the enhanced concentration of RNA and salt in liquid microenvironments within the ice. Freeze-thaw cycles and activating agents promote assembly of short RNA oligomers under conditions where degradation is minimized.
Substrate interactions by metabolic RNA: a double-site acting kinase ribozyme
Department of Molecular Microbiology and Department of Biochemistry, University of Missouri-School of Medicine, Columbia, MO - USA
A major goal of our research is to establish whether metabolic ribozymes are capable of sustaining life. We describe the characterization of a kinase ribozyme that promotes self-phosphorylation of two distinct 2' hydroxyls. The sites were mapped at the nucleotide level and the secondary structure of the active molecule was obtained by re-selection, SHAPE and extensive mutational analysis. The ribozyme’s activity is strictly ph-dependent and Mg2+ and Cu2+ ions are essential for optimal catalysis.
Domain Structure of the Ribosomal Large Subunit: The Search for Coopted RNA Structures in the Ribosome
1NASA Astrobiology Institute, United States of America; 2The Center for Ribosomal Origins and Evolution at the Georgia Institute of Technology, Atlanta, GA, United States of America; 3School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States of America; 4School of Biology, Georgia Institute of Technology, Atlanta, GA, United States of America
Our focus is the evolutionary implications of the domain structure of ribosomal RNA. We are deconstructing the Thermus thermophilus large subunit by systematically removing rRNA domains and their substructures to determine the effect of domain deletions on folding and assembly. In this manner, we hope to understand the evolutionary significance (or lack thereof) of individual domain structure, which may support models in which one more domains has an evolutionary origin distinct from other rRNA.
Spontaneous concentration and crowding of ribosomes and proteins inside liposomes: A model for the origin of primitive cells
1Biology Department University of Roma Tre, Italy; 2Institute of Pharmacy, FSU Jena, Germany; 3Elektronenmikroskopisches Zentrum, FSU Jena, Gemany
Lipid vesicles are often used as primitive cell models; solute encapsulation is the key step for the emergence a functional compartmentalized chemical system. In this contribution we report our recent investigation on the entrapment of proteins, ribosomes and multi-macromolecular systems as the transcription/translation machinery into lipid vesicles. Detailed electronmicroscopy study reveals the unexpected existence of vesicle that have captured a very high number of solute molecules.
Quantitative study and stochastic modeling of the physical and chemical heterogeneity in a population of cell-like compartments
1Biology Department University of Roma Tre, Italy; 2Chemistry Department, University of Bari, Italy
Stochastic effects are at the root of compartment formation and determine their size, content and reactivity of internalized reactions. Several studies have been carried out on compartment models but the study of these systems is often done by averaging the behavior of each compartment. Here we show that a more detailed experimental study on compartment diversity reveals the very nature of microcompartmentalized systems and allows a realistic stochastic modeling of its formation and dynamics.
Resurrection of Prebiotic Assemblies: Interactions of Ancestral rRNA with Ancestral Peptides
NASA Astrobiology Institute and the Center for Ribosomal Origins and Evolution at the Georgia Institute of Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA 30332-0400
The ribosome is an ancient biological machine, the fulcrum of evolution through translation of genotype to phenotype. We investigate the interactions of a working model of the ancestral ribosome with highly conserved amino acid sequences, sequences that our models suggest evolved concurrent with rRNA prior to coding and cooption of the small subunit. We investigate interactions in vitro and in vivo, describing a yeast three-hybrid system for recapitulation of the evolution of the ribosome.
Ribocell Population Modelling
Chemistry Department - University of Bari, Italy
The Ribocell is a minimal cell model based on a self-replicating minimum RNA genome coupled with a self-reproducing lipid vesicle compartment. This model assumes the existence of two hypothetical ribozymes one able to catalyze the conversion of molecular precursors into lipids and the second one able to replicate RNA strands. The aim of this contribution is to study the time behavior of a Ribocell Population by means of in silico stochastic simulations using kinetic parameters from literature.
In Vitro and in Silico Study of the Enzymatic Lipid Vesicles Time Behaviour
1Chemistry Department, University of Bari "Aldo Moro", Italy; 2Biology Department, University of Rome “RomaTre”, Italy
In this contribution the time behaviour of enzymatic pathways encapsulated in lipid vesicles will be presented and studied both with in silico and in vitro approach. The effect of stochasticity, both on the amount of the encapsulated enzyme per vesicle and on the average kinetic time course will be elucidated and discussed showing that it increases with the length of the pathway, i.e. with the number of different enzymatic steps involved.
Ribosomal Paleontology: Macromolecular Fossils from before Coded Protein
Georgia Institute of Technology, United States of America
The origins of the translation machinery remain imprinted in the extant ribosome. We describe new methods of ribosomal paleontology, to determine timelines for ribosomal origins. Ever-older molecular fossils are revealed as one bores into the center of the ribosome. The conformations of ribosomal protein components can be seen to change over time indicating clear molecular fossils of non-coded peptide ancestors of ribosomal proteins.
The ribonucleic acid world: did it evolve at low pH?
Tate lab, Biochemistry Dept, University of Otago, New Zealand
Life may have emerged in a low pH environment as early as during the Hadean Eon 4.3-3.8 Gyr ago, with a high level of atmospheric CO2 producing an ocean possibly as acidic as pH 4. Miyamoto and colleagues have suggested the RNA world may have occurred in such an acidic milieu. In support of this are the following observations: the selection of ribozymes active at low pH, the stability at low pH of RNA and the aminoacyl-tRNA bond, and the pH independence of peptide bond formation on the ribosome.
Small RNAs illuminate the dawn of coded protein synthesis
Tate lab, Biochemistry Dept, University of Otago, New Zealand
Specific catalysis is an inherent property of even extremely small RNAs, supporting the concept of a stage of evolution dominated by RNA. A 5-mer ribozyme has been discovered that aminoacylates an RNA 4-mer similar to the aminoacylated 3' CCA terminus of transfer RNA (tRNA), and 12- and 20-mer nuclear tRNA introns – protein spliced in vivo – have been shown to catalyze self-cleavage. These activities illuminate our model for the origin of the first tRNA and the dawn of coded protein synthesis.
Self-replicating Darwinian chemical systems
Harvard University, United States of America
The goal of our work is to identify and synthesize a nucleic acid molecule capable of spontaneous replication. Towards this goal, we have synthesized a series of phosphoramidite linked nucleic and evaluated their ability to undergo chemical replication. We present a series of experiments designed to understand key properties of non-enzymatic self-replicating systems including: self-assembly, template dependant/independent polymerization and copying fidelity.
2'-Amino-Threose Nucleic Acids as Potential Self-Replicating Polymers
1Department of Molecular Biology, Massachusetts General Hospital, Boston, MA; 2Department of Genetics, Harvard Medical School, Boston, MA; 3Howard Hughes Medical Institute
We have been exploring the chemistry of phosphoramidate nucleic acids and their phosphoroimidazolide activated monomers as self-replicating systems since their increased reactivity gives rapid non-enzymatic polymerization. Nucleic acids based on threose are promising candidates since their rigid backbone may give a pre-organized template for polymerization. We have developed a chemical synthesis of 2′-aminothreose nucleosides and are testing this system for non-enzymatic polymerization.
The Positive Cooperation of a GTPase and an Fe-S Protein: The Interaction of Two Functions Likely Present During Abiogenesis
Montana State University, United States of America
Hydrogen metabolism was likely an important process present at the origin of life. One enzyme of hydrogen metabolism is [FeFe]-hydrogenase, with a complex metallocaofactor that is biologically synthesized by two Fe-S containing radical SAM enzymes and one GTPase. We have recently shown a positive interaction exists between the radical SAM enzyme HydE and the GTPase HydF. HydE increases the GTPase activity of HydF by 50%, linking Fe-S systems and P-loop nucleotide triphosphate systems.
Replication of the Avocado sunblotch viroid in the Yeast Saccharomyces cerevisiae
Viroids are non-coding, “naked” RNAs, pathogenic for plant. Ancesters of viroids could have been present in an ancient RNA world. The Avsunviroidae family possess a hammerhead ribozyme. We demonstrate that an Avsunviroidae is able to self-cleave and to replicate in a unicellular host, the yeast S. cerevisiae. For the first time our results provide evidence that viroids can replicate in other organisms than plants, and raise the question of the presence of viroids in every living cell.
In vitro evolution of an RNA polymerase ribozyme
1Szostak Lab, Department of Genetics, Harvard Medical School, United States of America; 2Department of Chemistry and Chemical Biology, Harvard University, United States of America
How did RNA copy itself in the prebiotic world? Finding a plausible mechanism has been a goal in the field of prebiotic chemistry for decades. In order to address this problem I propose to run a novel in vitro selection to create sequence independent RNA polymerases. We will start with multiple ribozyme libraries based on various existing polymerases (and random sequence) and we will use different monomers to see if a ribozyme can be developed that will accept alternatives to rNTPs.
Convergence Pathways from Primordial Stochastic Origins to Primitive Genome-Directed Synthesis
University of North Florida, Department of Chemistry, Jacksonville FL USA
Transitions from stochastic primeval conditions to ordered metabolic synthesis before RNA are exemplified in the testing of a chemical information processor (CHIP) with chemical operating system (CHOS). In 50,000 emulations of CHIP+CHOS with 20 initial random data bits and 6 potential gene products linked to reproductive fitness, 9% develop bimodal cycles alternating gene replication with anabolism, enabling Darwinian evolution. We present patterns of genome convergence and fitness parameters.
CREATR: a complex, multistage model for the origin of life
1University College Dublin, Ireland; 2DigitalSpace, United States of America; 3University of California at San Diego
Complex Repeated Encapsulation of Attached Template Replicators (CREATR) is a conceptual multistage model of an origin of life. In this model viable protocell lines arise from a natural combinatorial chemistry experiments within compartments formed from membrane encapsulated micropores. Detached membranes form vesicles containing attached RNA complexes regulating vesicle growth, division and with chance combinations develop other innovations to extend protocell lines.
Stable Stacked Aggregates of Nitric Bases — First Genetics Matrixes
St-Petersburg State University
Earlier we have observed the stable stacking aggregates of nitric bases in water solutions (0.00001-0.01 M, pH 7.0), which did not dissociate even at 85°C . Now we have shown experimentally (by the luminescence method) that the aggregates work as matrixes in mixed solutions of Ade+Ura(Thy) at cyclic rises and falls of temperature from 2 to 7(6) °C.
 Rapoport V.L., V.M. Malkin, S.V. Zorina, S.M. Komarov, V.V. Goryuchko. Dokl. Akad. Nauk, 2006, Vol. 406, No. 3, 402-406).
Bacterial Plasmids – Relicts of RNA World?
St-Petersburg State University, Physics Department
Usually supposed, that based on the self-replicated polynucleotides ancient organisms, lived in the RNA World, died out after the appearance of the first cells. In biological world, after the appearance of more complicated species, the less complicated usually find new ecological niches. Where we can find relicts of the RNA World? It could be ancient symbionts, for example - bacterial plasmids, cyclic DNA chains, which can replicate his genetic material using resources of bacterial cell.
The Hammerhead Ribozyme, a “living fossil” of the RNA world
Acides Nucléiques Biophotonique, FRE3207 - CNRS, Université Pierre et Marie Curie - Paris
The original approach of hydrostatic pressure is used to study the conformational changes involved in the hammerhead ribozyme activity. We evidenced for the first time the presence in solution of different populations of structural isomers. We also searched for inhibitors of hammerhead ribozyme activity in a goal to hinder the viroid replication. We found that molecules bearing amino groups in particular ruthenium hexamine and spermine are among the most efficient inhibitors.
The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA
1Harvard University, United States of America; 2Department of Physics, Harvard University, Cambridge, MA 02138, USA; 3Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
The RNA world theory posits that RNA performed the duties of catalysis & information storage during a very early stage of life. The RNA world then transitioned to a DNA-RNA-protein world which included the ‘genetic takeover’ of information storage by DNA. We investigated evolutionary advantages for using DNA as the genetic material. Our results suggest that the 'genetic takeover' may have been driven by a combination of increased chemical stability, increased genome size, and irreversibility.