The Emergence of Life: From Chemical Origins to Synthetic Biology


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The Emergence of Life: From Chemical Origins to Synthetic Biology

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Be the first. Add a review and share your thoughts with other readers. Similar Items Related Subjects: 1 biologija -- evolucija -- zgodovinski preegled -- organske sinteze -- makromolekularne sekvence -- kiralnost verig -- reprodukcija -- nastanek celice -- avtopoieza sistemov. Linked Data More info about Linked Data. All rights reserved. Remember me on this computer. Cancel Forgot your password? Pier Luigi Luisi. Print book : English View all editions and formats. Similar Items. Preface; 1.


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The conceptual framework of the research on the origin of life on Earth; 2. Approaches to the definitions of life; 3. Selection in prebiotic chemistry - why this The bottle neck - macromolecular sequences; 5. Self-organization; 6. Emergence and emergent properties; 7.

Self-replication and self-reproduction; 8. Autopoiesis - the logic of cellular life; 9. Compartments; Reactivity and transformation of vesicles; Novel reports have highlighted the role of combinatorial design to produce and select residues long proteins with capability of sustaining E. Knowing the firm relation between structure and function of biological molecules we decided to precede the random RNAs functional exploration with some structural studies using the RNA Foster RNA folding stability test.

The Foster is capable to quantitatively determine the fraction of folded RNAs in function of temperature De Lucrezia et al. It employs a specific nuclease S1; Vogt, to cleave at different temperatures single-strand RNA sequences, monitoring the presence of double-stranded domains and indirectly any possible structure. In fact, folded RNAs are more resistant to S1 nuclease than unfolded ones, namely the latter are degraded faster than the former. In addition, we exploited the capability of nuclease S1 to work over a broad range of temperatures to probe RNA secondary domain stability at different conditions.

In fact, an increase in temperature destabilizes the RNA fold, inducing either global or local unfolding.

The Emergence of Life

Consequently, the RNA becomes susceptible to nuclease attack and is readily degraded De Lucrezia et al. In few words the most stable sequences at high temperature will be those with a more stable secondary and possibly tertiary structure. So far, the most general result of our studies lies in the demonstration that RNAs have the capacity to fold into compact secondary structures, even in absence of selective pressure Anella et al. This confirm our hypothesis that molecules involved in nowadays life do not have exclusive features as far as the ability to adopt a stable fold is concerned.

These results are absolutely outstanding and can be used to provide directions and suggestions for further studies concerning the functional properties of RNAs, in the early evolution scenario as well. In our laboratory we are trying to study more in detail the structure characteristic of NBRNA using more complex libraries and secondary and tertiary structure predictions as well as spectroscopic methods.

The Emergence Of Life: From Chemical Origins To Synthetic Biology By Pier Luigi Luisi

When we look at modern living cells it is difficult not to remain astonished by the beautiful complexity of thousands of intricate genetic—metabolic complexes occurring in the tiny cellular environment, and we ask how this complexity was originated by spontaneous generation and later shaped by the evolution. How can we study such simple and primitive cells?

These biological entities do not exist any more in nature, and therefore the synthetic constructive approach — typical of CSB — is the only way to get insights into the physical and chemical constraints that ruled the emergence of early cells in ancient times. However, any attempt to construct a complex system such as a living — yet primitive — cell needs the knowledge of the minimal biological organization that characterizes life. In this context, the theory of autopoiesis, introduced in the s by Humberto Maturana and Francisco Varela Varela et al.

Autopoiesis self-production says that a living cell is a physical object composed by reactive molecules , which: 1 distinguishes itself from the environment thank to a well-defined semi-permeable boundary, 2 encloses networks of reactions that transform the precursors available in the environment in the same molecules that form the reaction network, 3 despite the continuous turnover of its molecular constituents, the autopoietic system maintain its own identity in terms of dynamic and spatial organization.

Thanks to these theoretical guidelines, can we build minimal autopoietic cells in the laboratory? One possibility is the construction of minimal cells basing on allegedly primitive molecules, such as fatty acids, ribozymes, simple primitive peptides. A simple ribozyme-in-liposome model has been proposed Szostak et al. Another possibility deals with totally synthetic systems, based for example on polymers, PNAs, elaborated transition metal catalysts, etc. Rasmussen et al.


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  8. Water-in-oil emulsion droplets, where compartmentalized reactions can be carried out, as pioneered by Tawfik and Griffiths , are also alternative synthetic systems to build cellular models, but they lack of the semi-permeable lipid bilayer that characterizes biological cells. We believe that a third way is actually the most fruitful one, because it has been successfully used to shed light on the emergence primitive cells, and at the same time it promises remarkable applications in biotechnology Jewett and Forster, , nanomedicine Leduc et al.

    Currently this approach stems from the convergence of liposome technology and cell-free technology and it is investigated by several groups, as witnessed by the richness of the recently published original work Budin et al. Semi-synthetic minimal cells. A Semi-synthetic minimal cells are based on the encapsulation of the minimal number of biological molecules, like DNA, ribosomes, tRNAs, enzymes, amino acids, nucleotides, etc.

    Currently it is possible to encapsulate the whole transcription—translation machinery so that proteins are synthesized inside the synthetic cell. The goal of research is the self-reproduction of the minimal cells thanks to the simultaneous and possibly coupled production of internal and membrane components. Reproduced from Chiarabelli et al.


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    B Confocal fluorescence image of a liposome, prepared by the droplet transfer method, which contains the whole transcription—translation machinery E. In this case, the enhanced green fluorescence protein eGFP was synthesized, as evidenced by the green fluorescence. C The liposome membrane were made visible after Trypan blue addition, which binds to phospholipid bilayers and becomes red fluorescent upon nm excitation.

    D,E Quantitation of fluorescence along the yellow lines in B,C gives typical bell-shaped and U-shaped profiles, respectively, for water-soluble eGFP and membrane-bound Trypan blue fluorochromes. For example, several studies revealed that the essential housekeeping functions of living cells are encoded in a minimal number of genes, around Gil et al.

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    About one half of the minimal genome is devoted to the specification of proteins and RNAs dedicated to the protein synthesis, without doubts the most important process, together the nucleic acid replication and the lipid synthesis but consider that the latter two processes are only possible thank to enzymes. It is therefore not quite surprising that the current state-of-the-art in minimal cell research focuses on protein synthesis inside liposomes.

    Several advancements have been reported from the time of the pioneer report from Oberholzer et al. Most of the more recent studies are carried out by incorporating — inside liposomes — of the minimal number ca. The low yield associated to the involvement of the membrane enzymes that catalyze these transformations has prevented efficient lipid production, so that the direct observation of a spontaneous growth and division due to intraliposome lipid production is still missing.

    There are, however, novel and intriguing advancements in exploring the emergence of minimal cells from separated components. In fact, we recently investigated in details the physics of solute encapsulation inside liposomes spontaneously formed by lipid self-assembly — a key event for the emergence of primitive cells. Driven by our intriguing observations on the success of solute encapsulation and protein synthesis inside nm diameter vesicles Souza et al. By using ferritin, ribosomes, and ribo-peptidic complexes, we revealed the true intraliposome solute distribution by direct counting the number of entrapped macromolecules via cryo-transmission electron microscopy Luisi et al.

    In other words, liposomes can spontaneously concentrate macromolecular solutes in their cavity, providing a mechanism for the emergence of cellular metabolism even starting from a diluted solution. In fact, this mechanism might provide a rational explanation on the onset of intraliposome complex reactions that cannot occur in bulk phase due to extreme dilution. We have recently assayed such realistic scenario by using the synthesis of green fluorescent protein synthesis as a metabolic model Stano et al.

    An additional dimension has been added to SB, namely the CSB approach, based on the concept of producing biological structures alternative to the natural ones, by using chemical and biochemical technology. The corresponding investigations are based, respectively, on the exploration of peptide- and RNA-libraries, and on the encapsulation of solutes inside lipid vesicles.

    These approaches give a rather rich variety of novel forms and corresponding novel ideas, which may be relevant for understanding how biological systems are constructed and works, as well as for potentially new biotechnological applications. NBRNAs might become novel therapeutical agents. Minimal cells, when properly designed, might find applications in advanced drug delivery approaches, and would not only serve as model or primitive cells.

    CSB is a large field in which basic science and applicative research combine together, and we are confident that it will bring about significant advancements. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. National Center for Biotechnology Information , U.

    Journal List Front Microbiol v. Front Microbiol. Published online Sep Author information Article notes Copyright and License information Disclaimer. This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology. Received Jun 5; Accepted Sep 4. The use, distribution or reproduction in other forums is permitted, provided the original author s or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.

    No use, distribution or reproduction is permitted which does not comply with these terms. This article has been cited by other articles in PMC.

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    Abstract Chemical synthetic biology CSB is a branch of synthetic biology SB oriented toward the synthesis of chemical structures alternative to those present in nature. Keywords: liposomes, minimal cell, protein folding, random sequence, RNA stability, synthetic biology, synthetic cells. Open in a separate window. Conflict of Interest Statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Competition between model protocells driven by an encapsulated catalyst.

    Targeting Listeria monocytogenes rpoA and rpoD genes using peptide nucleic acids.

    The Emergence of Life: Second Edition

    Nucleic Acid Ther. Synthetic biology: new engineering rules for an emerging discipline. Growth and transformation of vesicles studied by ferritin labeling and cryotransmission electron microscopy. B —

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