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Archive for the ‘Allegretti’ Category

ON EVOLUTION OF PRIMEVAL MEMBRANE PROTEINS

In Allegretti on July 9, 2013 at 2:11 PM

It is easy to note, while looking for the most conserved proteins, an under-representation of early conserved membrane proteins. This fact suggests that the emergence of membrane proteins may have followed the emergence of pre-cellular RNA/protein organisms. However, the nearly universal conservation of complex, membrane-embedded molecular machines, such as general protein secretory pathway elements and the F- and V-type ATP-synthases in modern cellular life forms, indicates that the L.U.C.A. might possess some kind of hydrophobic layer although not necessarily a full-fledged cellular organization based on lipid biosynthesis.The energetics of first living forms had to have been based on phosphate transfer reactions, since all the organisms were depending on nucleotides-triphosphate as energy source for anabolic reactions, synthesized mostly by ATP-synthases. Likely, the ancestral ATP-synthases, the smallest existing rotary engines, evolved from the connection of a membrane hexameric helicases (like the RNA-helicase Rho) with a membrane pore, and proceeded through the stages of RNA and protein translocases pumping sodium ions along with other sodium-pumps, such as the sodium-transporting pyrophosphatase and the sodium-transporting decarboxylase (present both in bacteria and archaea, antedating therefore the divergence of the three domains of life). Concerning the formation of a pore into the membrane, a helical hairpin, upon an succeeding interaction with a double-layer, might spread on its surface and then reassemble within the membrane in such a way that the non-polar side chains would interact with the hydrophobic lipid phase. More hairpins, then, would tend to aggregate, leading to the formation of water-filled pores. This arrangement is retained by the membrane embedded ring of the ATP-synthases, while the described mechanism of spontaneous protein insertion into the membrane (without translocon machinery) is still used by certain bacterial toxins and related proteins. Unlike other sodium-pumps, this common ancestor of the F/V-ATP-synthases would be potentially able to translocate sodium ions in both directions, thus resulting a reversal of the rotation in a sodium-driven synthesis of ATP. It is probable that the fulfillment of this event marked the birth of membrane bioenergetics, when the ancient sodium-pumps, together with the ancestral F/V-type ATP synthases, completed the first bioenergetic cycle. At a later stage, there would have been a transition towards a proton driven bioenergetics with the evolution of tighter membranes (possessing two-chains lipids for instance), where proton transfer could have been chemically coupled to redox reactions, thus enabling the creation of efficient redox- and light-driven generators of a proton motive force. The second possibility for the formation of integral membrane proteins would be the creation of membrane pores from large amphiphilic proteins, which might undergo “inside-out” rearrangements after binding to lipid bilayers. The second universally conserved membrane protein, SecY, exemplifies this kind of protein architecture. Starting from the pores that were built up of amphiphilic stretches of amino acids, such integral membrane proteins could evolve via the combined effect of multiple replacements of polar amino acids and gene duplications, ultimately yielding multi-helix hydrophobic bundles. Then, these multi-helix bundles could enable the controlled insertion of hydrophobic bundles into the membrane (with the aid of other proteins), as in the case of the conserved translocon SecY. Therefore, a plausible scenario of membrane evolution should include an evolutionary scenario for the emergence of integral membrane proteins, in parallel with the cellular lipid synthesis: in this way it suggests a co-evolution between inner cellular biochemical pathways, and the membrane system (the latter is a system because it consists of lipid bilayer plus different kinds of embedded proteins). Such co-evolutionary process, as above anticipated, brought about an increase in the ion-tightness of the membrane, and a transition from amphiphilic, pore-forming proteins, towards highly hydrophobic integral membrane complexes, which are very efficient for specific functions. Unfortunately, a comparison between bacteria and archaea does not shed much light on the origin and evolution of biological membranes, since the two domains have diverged too early in the complexification of their membranes.

Matteo Allegretti

Bibliography

 

Koonin, E.V., Martin, W. (2005) On the origin of genomes and cells within inorganic compartments; Trends Genet., 21, 12: 647-54.

Mulkidjanian, A.Y., Galperin, M.Y., Koonin, E.V. (2009) Co-evolution of primordial membranes and membrane proteins; Trends Biochem Sci., 34, 4: 206-15.

Mulkidjanian, A.Y., Makarova, K.S., Galperin, M.Y., Koonin, E.V. (2007) Inventing the dynamo machine: the evolution of the F-type and V-type ATPases; Nat Rev Microbiol., 5, 11: 892-9.

ON EVOLUTION OF PRIMEVAL LIFE (2nd part)

In Allegretti on June 18, 2013 at 11:24 AM

The first proto-L.U.C.A. was probably not a typical membrane-bound cell, but rather a coordinated consortium of replicating genetic elements (maybe some virus-like particles) that might dwell in networks of inorganic compartments, as described in the first part of the article.

F) Inorganic zinc sulfides were likely good candidates for the early formation of such primeval enclosed compartments. Moreover, zinc sulfide was also a very powerful photo-catalyst that could reduce CO2  to formate (precursor of other organic compounds including intermediates of the Krebs cycle) and drive various transformations of nitrogen containing substrates. Posteriorly, single-chain fatty acids and prenyls (reported both in meteorites), could spontaneously self-assemble into leaky vesicles, allowing exchanges of metabolites. The self-organization of lipid compartments from a chaotic mixture of amphipathic monomers (due to thermodynamic reasons) was a nodal event in the evolution of cell-life, these double-layer membranes could in fact undergo spontaneous growth and division and at the same time they provided a protective and discriminative shell permeable to small substrates as nucleotides and aminoacids.

G) Stanley Miller and his colleagues showed that simple building blocks such as amino acids, nitrogenous bases and carbohydrates, could be produced from inorganic compounds under conditions imitating the primordial atmosphere, as long as energy was provided in the form of electric discharges or UV light. In addition, typical primordial compounds like carbonyl sulfides were catalysts of peptide bond formation (as some ribozymes and dipeptides).

H) With the evolution of the first proto-cells, division was probably either mechanical by shearing forces, due to an abundance of amphiphilics in the medium, or simply due to the evaporation of water, which could favor division by mechanical stress. Furthermore, RNA encapsulated in vesicles could exert an osmotic pressure on the vesicle membrane, driving the uptake of additional membrane components from some vesicles at the expense of other, shrinking ones. Thus, more efficient RNA replication could cause a faster cellular growth, leading to the emergence of Darwinian evolution at a proto-cellular level.

I) Eventually, the interactions between RNA and peptides would have brought to the appearance of the first genetic code (possibly only a two letters code) and the first ribosomal, RNA-catalyzed protein synthesis (probably with a reduced amino acid alphabet).

J) The replication of the content of the vesicles (for instance ribozymes and peptides) soon became coupled with the growth and division of the proto-cell, due probably to the evolution of very versatile proteinaceous-enzymes, that could have taken over RNA’s role in assisting genetic copying and in other biochemical processes.

K) At a later stage, the organisms “learned” to make DNA, gaining the advantage of possessing a more robust carrier of genetic information. The “RNA world” became therefore the “DNA world” and, most likely at that point, lipid biosynthesis became self-made by the cell.

L) With the evolution of bulky polar lipids and so tighter membranes able to maintain ion gradients, the first cells could escape the geothermal fields and invade terrestrial water basins with low potassium/sodium (K+/Na+) ratio like rivers and oceans (first free-living L.U.C.A.).

At that moment, coordination between the inner content and the surface of the cell was already present, and the membrane was as of now a system of transportation and channeling containing some integral and peripheral membrane proteins. Unfortunately it has not yet been clarified how this coordination is linked to the evolution of membrane proteins themselves. Nevertheless, since the organization of the living system emerged in a way that its own survival was inevitably intertwined with the medium, membrane proteins evolved coupling probably from the beginning the inner cell biochemical processes with the external environment (primeval cognition). This structural/functional integration is a historical, dialogic product of interactions that allow to maintain the autonomy of living systems through regulated exchanges of matter and energy with the outside. Nonetheless, drastic (predictable or unpredictable) perturbations of the plastic, but fragile, whole-equilibrium could affect the rate of compensation and adaptation of living organisms, bringing about complex, evolutionary changes, which could end (in a broader prospect) in species rearrangements of the planetary ecosystem.

Matteo Allegretti

 

Bibliography

 

Bich, L., Damiano, L. (2012) Life, autonomy and cognition: an organizational approach to the definition of the universal properties of life; Orig Life Evol Biosph. 42, 5: 389-97.

Chen, I.A., Roberts, R.W., Szostak J.W. (2004) The Emergence of Competition Between Model Protocells; Science, 305, 5689: 1474-6. 

Hanczyc, M.N., Fujikawa, S.M., Szostak J.W. (2003) Experimental models of primitive cellular compartments: Encapsulation, growth, and division; Science, 302: 618–622.

Koonin, E.V., Martin, W. (2005) On the origin of genomes and cells within inorganic compartments; Trends Genet., 21, 12: 647-54.

Koonin, E.V., Mulkidjanian, A.Y. (2013) Evolution of cell division: from shear mechanics to complex molecular machineries; Cell, 152, 5: 942-4.

Kurihara, K., Tamura, M., Shohda, K., Toyota, T., Suzuki, K., Sugawara, T. (2011) Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA; Nat Chem., 3, 10: 775-81. 

Mulkidjanian, A.Y., Galperin, M.Y. (2007) Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life; Chem Biodivers., 4, 9: 2003-15.

Mulkidjanian, A.Y., Bychkov, A.Y., Dibrova, D.V., Galperin, M.Y., Koonin, E.V. (2012)  Open questions on the Origin of Life at Anoxic Geothermal Fields; Orig Life Evol Biosph., 42, 5: 507-16.

Szostak, J.W., Bartel D.P., Luisi P.L. (2001) Synthesizing life; Nature, 409, 6818: 387-90.

ON EVOLUTION OF PRIMEVAL LIFE (1st part)

In Allegretti on June 18, 2013 at 8:49 AM

Dealing with “life” and its origins from an epistemological and empirical point of view implies a phenomenological, historical description, dependent on the experience domain of the observer. Primordial, compartmentalized (membrane-delimited) life appears as a dissipative (operating far from thermodynamic equilibrium), open kind of organization originated between 3.5 and 3.8 billions of years ago, i.e. when the first fossils of prokaryotes are dated. The starting point was probably some inorganic matter, which spontaneously self-assembled and underwent a “molecular evolution” in the contingent environmental conditions with the constraints imposed by physical and chemical laws. Both experimental (simplification of existing prokaryotes and synthesis of proto-living systems from plausible pre-biotic molecules) and theoretical (nucleotide dynamics and cellular behavior simulations) approaches are actively involved in understanding how the first living prokaryotes emerged, trying to obtain in vitro the main properties of a living entity: self-reproduction, self-maintained organization and possibility to evolve. In addition, every kind of transition from chemistry to biology has to consider the support of an energy flow and metabolites from the external environment. Obviously, the number of hypothetical, contingent scenarios for the origin of life is virtually unlimited, but it is easy to imagine that the pathway was complex, discontinuous and full of trials. The fashion of this kind of research (a small section of the broad field of synthetic biology/artificial life) comes also from this relative freedom and creativeness in the experimental setting. First living cellular systems, in a systemic conceptual framework, were born up-taking from the environment chemical precursors and transforming them in such a way that the product of these transformations was ultimately a “close identity” (despite a variety of perturbations and the continuous changes of its components) consisting of a network of functionally related biochemical processes topologically distinct by a semi-permeable boundary (later self-made). The evolution of such persistent metabolic pathways in the first living systems is therefore indissolubly linked and dependent from the external environment, in fact, cell metabolism is the result of a dynamic interaction with the medium, which feeds the cell and accepts expelled byproducts through the boundary. The cellular system and the environment trigger changes and adaptations one with the other in a congruent way (primeval cognition), and, in this co-emergent dependency, the living system autonomy is surprisingly maintained through generations thanks to a complex multi-regulated and multi-pattern framework. Let’s try in the following lines to trace an approximate and not sequential pathway that brought to the origin of proto-living entities trying to emphasize both the molecular and the system evolution.

A) Several groups reported the formation and oligomerization of cyclic ribonuclotides in formamide solutions under UV radiation in the presence of phosphorous compounds in anoxic geothermal fields. These photostable, cyclic ribonucleotides could represent the monomers and the energy source for the abiotic formation of RNA replicators/ribozymes around 4 billions of years ago. The formation of phosphodiester bonds was favored by the ability of potassium and zinc ions (high quantity in geothermal fields) to catalyze transphosphorilation reactions.

B) Mineral/clay and lipid surfaces could serve as templates/catalyst for the abiotic synthesis of short/long organic molecules/polymers and their replication.

C) Geothermal fields were also full of water, silica, metal sulfides and amphiphilic molecules that could produce honeycomb porous reactors. Such porous membranes could naturally favor horizontal gene mixing and sharing of metabolites among the first proto-life forms (co-development). Some of these primitive compartments could have the possibility to encase a large amount of short/long RNA-replicators, which could remain viable if connected via metabolic networks.

D) The process of RNA replication could be favored in volcanic regions on the cold surface of the early earth where the temperature differences would cause convection currents, so that nucleic acids possibly encapsulated in proto-compartments would be often exposed to a burst of heat as passing near the hot rocks. This event would cause a double helix to separate into single strands, but they would almost instantly cool down again (as the heated water came across the bulk of cold one) forming new double strands, copies (with some mutations) of the original ones. In addition, mixtures of RNA fragments, after self-assemblage into self-replicators, spontaneously could form catalytic cycles. Such networks can grow very fast indicating an intrinsic ability of RNA populations to evolve through cooperation giving birth to hyper-cycles (different self-replicative informational cycles which interact and cooperate one with the other).

The replicating moieties of one inorganic bubble at a hydrothermal vent, sharing a common pool of metabolites and genes, could resemble a distinct evolutionary unit able of Darwinian selection and, eventually separable as an enclosed system. The emergence of L.U.C.A. (last universal common ancestor) was at that moment not so far.

Matteo Allegretti 

Bibliography

Bich. L., Damiano, L. (2012) On the emergence of biology from chemistry: a discontinuist perspective from the point of view of stability and regulation; Orig Life Evol Biosph, 42, 5: 475-82.

Carrara, P., Stano, P., Luisi, P.L. (2012) Giant Vesicles “Colonies”: A Model for Primitive Cell Communities; Chembiochem, 13, 10: 1497-502.

Chen. I., Nowak M.A. (2012) From Prelife to Life: How Chemical Kinetics Become Evolutionary Dynamics; Accounts of chemical research, 45, 12: 2088-2096.

De Souza, T.P., Steiniger, F., Stano, P., Fahr, A., Luisi, P.L. (2011) Spontaneous crowding of ribosomes and proteins inside vesicles: a possible mechanism for the origin of cell metabolism; Chembiochem., 12, 15: 2325-30.

Dibrova, D.V., Chudetsky, M.Y., Galperin, M.Y., Koonin, E.V., Mulkidjanian, A.Y. (2012) The role of energy in the emergence of biology from chemistry; Orig Life Evol Biosph., 42, 5: 459-68.

Eigen, M., Schuster, P. (1978) Hypercycle – Principle of natural self-organization. A. Emergence of hypercycle; Naturwissenschaften 64: 541–565. 

Koonin, E.V., Martin, W. (2005) On the origin of genomes and cells within inorganic compartments; Trends Genet., 21, 12: 647-54.

Luisi, P.L. (2006) The Emergence of Life: From Chemical Origins to Synthetic Biology; Cambridge University Press.

Mulkidjanian, A.Y., Galperin, M.Y. (2007) Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life; Chem Biodivers., 4, 9: 2003-15. 

Mulkidjanian, A.Y., Bychkov, A.Y., Dibrova, D.V., Galperin, M.Y., Koonin, E.V. (2012) Open questions on the Origin of Life at Anoxic Geothermal Fields; Orig Life Evol Biosph., 42, 5: 507-16.

Olasagasti, F., Kim, H.J., Pourmand, N., Deamer, D.W. (2011) Non-enzymatic transfer of sequence information under plausible prebiotic conditions; Biochimie, 93, 3: 556-61.

Orgel, L.E. (2004) Prebiotic Chemistry and the Origin of the RNA World; Crit. Rev. Biochem. Mol. Biol., 39, 2: 99-123

Prigogine, I., Nicolis, G. (1977) Self-Organization in Non-Equilibrium Systems; Wiley. ISBN 0-471-02401-5.

Ricardo, A., Szostak, J.W. (2009) Origin of life on earth; Sci Am., 301, 3: 54-61.

Vaidya, N., Manapat, M.L., Chen, I.A., Xulvi-Brunet, R., Hayden, E.J., Lehman, N. (2012) Spontaneous network formation among cooperative RNA replicators; Nature, 491, 7422: 72-77.