Measuring the tolerance of the genetic code to altered codon size

SummaryProtein translation using four-base codons occurs in both natural and synthetic systems. What constraints contributed to the universal adoption of a triplet-codon, rather than quadruplet-codon, genetic code? Here, we investigate the tolerance of the E. coli genetic code to tRNA mutations that increase codon size. We found that tRNAs from all twenty canonical isoacceptor classes can be converted to functional quadruplet tRNAs (qtRNAs), many of which selectively incorporate a single amino acid in response to a specified four-base codon. However, efficient quadruplet codon translation often requires multiple tRNA mutations, potentially constraining evolution. Moreover, while tRNAs were largely amenable to quadruplet conversion, only nine of the twenty aminoacyl tRNA synthetases tolerate quadruplet anticodons. These constitute a functional and mutually orthogonal set, but one that sharply limits the chemical alphabet available to a nascent all-quadruplet code. Our results illuminate factors that led to selection and maintenance of triplet codons in primordial Earth and provide a blueprint for synthetic biologists to deliberately engineer an all-quadruplet expanded genetic code.

Expansion-Oriented View On Origin of Oceans

Both the concepts of plate tectonics and continental drift conceive that the planet earth’s dimension, associated with its oceans, has remained unchanged throughout the past geological periods. In contrast, Hilgenberg’s model of earth expansion endorses that initially the planet was considerably small and devoid of oceans [1]. Based on earth expansion theory the author has pointed out that since the primordial condensed or small earth was devoid of oceans, initially the ocean-forming water must have been associated with the mantle, thereby turning that geosphere considerably fluid and pre-eminently suitable for planetary expansion. Expansion of the planet appears to have been caused owing to swelling up of the semi-fluid mantle in response to an external gravitational pull caused by an extra-terrestrial planetary body, probably the Moon. The primordial earth was completely covered with a relatively thin granitic crust, which, due to swelling up of the mantle developed a number of long and sinuous expansion cracks. Through these expansion cracks widespread eruption of molten magma took place spreading on both sides of the cracks to form rudimentary oceans basins. With continued expansion, the dimension of the oceans was broadened while the expansion cracks turned in to mid-oceanic ridges. Associated with expulsion of molten lava, large quantum of volatiles, chiefly constituted of water was released from the mantle that formed the ocean water while due to desiccation of the mantle, the process of expansion was eventually stopped.

Streamer discharges in the atmosphere of Primordial Earth

<p>Motivated by the Miller-Urey experiment suggesting that lightning may have contributed to the origin of life on Earth through the formation of amino acids and carbonic acids, we here investigate the occurrence of electric discharges in the atmosphere of Primordial Earth. We focus on the early stages of lightning in the atmosphere of Primordial Earth, the so-called streamers, thin ionized plasma channels.</p><p>We study electron avalanches and potential avalanche-to-streamer transitions by modeling the motion of electrons with a particle-in-cell Monte Carlo code in gas mixtures of H<sub>2</sub>O:CH<sub>4</sub>:NH<sub>3</sub>:H<sub>2</sub>=37.5%:25%:25%:12.5% [S. L. Miller. Production of Some Organic Compounds under Possible Primitive Earth Conditions. Am. Chem. Soc., 77:9, pp. 2351-2361 (1955)] and N<sub>2</sub>:CO<sub>2</sub>:H<sub>2</sub>O:H<sub>2</sub>:CO=80%:18.89%:1%:0.1%:0.01% [J. F. Kasting. Earth’s Early Atmosphere. Science, 259:5097, pp. 920-926 (1993)] suggested for Primordial Earth approx. 3.8 Ga ago in different electric fields and for different levels of background ionization mimicking the photoionization process. We compare the evolution of the electron density,  electric field, and electron energies with those for Modern Earth. Finally, we will discuss which conditions favour streamer inception, as well as consequences for discharges on Primordial Earth.</p>

Heme A-containing oxidases evolved in the ancestors of iron oxidizing bacteria

The origin of oxygen respiration in bacteria has long intrigued biochemists, microbiologists and evolutionary biologists. The earliest enzymes that consume oxygen to extract energy did not evolve in the same lineages of photosynthetic bacteria that released oxygen on primordial earth, leading to the great oxygenation event (GOE). A widespread type of such enzymes is proton pumping cytochrome c oxidase (COX) that contains heme A, a unique prosthetic group for these oxidases. Here we show that the most ancestral proteins for the biosynthesis of heme A are present in extant acidophilic Fe2+-oxidizing Proteobacteria. Acidophilic Fe2+-oxidizers lived on emerged land around the time of the GOE, as suggested by the earliest geochemical evidence for aerobic respiration on paleoproterozoic earth. The gene for heme A synthase in acidophilic Fe2+-oxidizing Proteobacteria is associated with the COX gene cluster for iron oxidation. Compared to many other soil bacteria, the COX subunits encoded by this gene cluster are early diverging. Our data suggest that the ancient bacterial lineage which first evolved heme A-containing COX was related to the ancestors of present acidophilic Fe2+-oxidizers such as Acidiferrobacter and Acidithiobacillus spp. The copper leaching activity of such bacteria might have constituted a key ecological factor to promote COX evolution.

Carbonyl Sulfide-Mediated Synthesis of Peptides with Amino Acid Ionic Liquids

Carbonyl sulfide (OCS), the component of volcanic emission, has been found to induce the condensation of amino acids under simulated primordial earth conditions. However, the applications of OCS in peptide chemical synthesis is still limited by their heterogeneities and low efficiencies. We herein report an OCS-mediated approach for solid-phase peptide synthesis using amino acid ionic liquids as recyclable reactants. The coupling reactions required no base and solvent and was completed in minutes at room temperature. The applicability and sustainability of this approach were demonstrated by the facile syntheses of peptides with remarkably high yields.

Carbonyl Sulfide-Mediated Synthesis of Peptides with Amino Acid Ionic Liquids

Carbonyl sulfide (OCS), the component of volcanic emission, has been found to induce the condensation of amino acids under simulated primordial earth conditions. However, the applications of OCS in peptide chemical synthesis is still limited by their heterogeneities and low efficiencies. We herein report an OCS-mediated approach for solid-phase peptide synthesis using amino acid ionic liquids as recyclable reactants. The coupling reactions required no base and solvent and was completed in minutes at room temperature. The applicability and sustainability of this approach were demonstrated by the facile syntheses of peptides with remarkably high yields.

A Minimalistic Hydrolase Based on Co-Assembled Cyclic Dipeptides

This paper describes minimalistic cyclic dipeptides acting as esterase-mimicks in a self-assembled hydrogel state. It demonstrates that cyclic dipeptides could have acted as enzyme-precursors on a primordial earth and hence be important for abiogenesis. <br>

A Minimalistic Hydrolase Based on Co-Assembled Cyclic Dipeptides

This paper describes minimalistic cyclic dipeptides acting as esterase-mimicks in a self-assembled hydrogel state. It demonstrates that cyclic dipeptides could have acted as enzyme-precursors on a primordial earth and hence be important for abiogenesis. <br>