scholarly journals From chemical metabolism to life: the origin of the genetic coding process

2017 ◽  
Vol 13 ◽  
pp. 1119-1135 ◽  
Author(s):  
Antoine Danchin

Looking for origins is so much rooted in ideology that most studies reflect opinions that fail to explore the first realistic scenarios. To be sure, trying to understand the origins of life should be based on what we know of current chemistry in the solar system and beyond. There, amino acids and very small compounds such as carbon dioxide, dihydrogen or dinitrogen and their immediate derivatives are ubiquitous. Surface-based chemical metabolism using these basic chemicals is the most likely beginning in which amino acids, coenzymes and phosphate-based small carbon molecules were built up. Nucleotides, and of course RNAs, must have come to being much later. As a consequence, the key question to account for life is to understand how chemical metabolism that began with amino acids progressively shaped into a coding process involving RNAs. Here I explore the role of building up complementarity rules as the first information-based process that allowed for the genetic code to emerge, after RNAs were substituted to surfaces to carry over the basic metabolic pathways that drive the pursuit of life.

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Kamm ◽  
Hans-Jürgen Osigus ◽  
Peter F. Stadler ◽  
Rob DeSalle ◽  
Bernd Schierwater

AbstractSymbiotic relationships between eukaryotic hosts and bacteria range from parasitism to mutualism and may deeply influence both partners’ fitness. The presence of intracellular bacteria in the metazoan phylum Placozoa has been reported several times, but without any knowledge about the nature of this relationship and possible implications for the placozoan holobiont. This information may be of crucial significance since little is known about placozoan ecology and how different species adapt to different environmental conditions, despite being almost invariable at the morphological level. We here report on the novel genome of the rickettsial endosymbiont of Trichoplax sp. H2 (strain “Panama”). The combination of eliminated and retained metabolic pathways of the bacterium indicates a potential for a mutualistic as well as for a parasitic relationship, whose outcome could depend on the environmental context. In particular we show that the endosymbiont is dependent on the host for growth and reproduction and that the latter could benefit from a supply with essential amino acids and important cofactors. These findings call for further studies to clarify the actual benefit for the placozoan host and to investigate a possible role of the endosymbiont for ecological separation between placozoan species.


Life ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 58 ◽  
Author(s):  
Pol Arranz-Gibert ◽  
Jaymin R. Patel ◽  
Farren J. Isaacs

The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino acids (nsAAs) into proteins. A key challenge for robust genetic code expansion is orthogonality; the engineered machinery used to introduce nsAAs into proteins must co-exist with native translation and gene expression without cross-reactivity or pleiotropy. The issue of orthogonality manifests at several levels, including those of codons, ribosomes, aminoacyl-tRNA synthetases, tRNAs, and elongation factors. In this concept paper, we describe advances in genome recoding, translational engineering and associated challenges rooted in establishing orthogonality needed to expand the genetic code.


1956 ◽  
Vol 34 (1) ◽  
pp. 511-519 ◽  
Author(s):  
G. H. N. Towers ◽  
D. C. Mortimer

Of the keto acids identified in leaves of sugar beet and other plants exposed to C14O2, pyruvic acid was found to be the only one labelled in light periods up to 45 sec. α-Ketoglutaric and glyoxylic acids became radioactive after about 45 sec. Radioactive hydroxypyruvate was not identified under these conditions and labelled oxaloacetate was detected only in trace amounts after 60 sec. in Scenedesmus. In contrast glycine and serine were labelled after 10 sec. under comparable conditions and aspartic acid was appreciably labelled after 30 sec. The effect on the radioactivity of the keto acids of an additional period intracer-free air, with and without light, as well as the dark incorporation of C14O2 was studied. These results are discussed in relation to the role of the ketoacids in photosynthesis. It is concluded that the synthesis of amino acids such as glycine, serine, and aspartic acid may be effected by mechanisms other than transamination in green leaves in the light.


1956 ◽  
Vol 34 (3) ◽  
pp. 511-519 ◽  
Author(s):  
G. H. N. Towers ◽  
D. C. Mortimer

Of the keto acids identified in leaves of sugar beet and other plants exposed to C14O2, pyruvic acid was found to be the only one labelled in light periods up to 45 sec. α-Ketoglutaric and glyoxylic acids became radioactive after about 45 sec. Radioactive hydroxypyruvate was not identified under these conditions and labelled oxaloacetate was detected only in trace amounts after 60 sec. in Scenedesmus. In contrast glycine and serine were labelled after 10 sec. under comparable conditions and aspartic acid was appreciably labelled after 30 sec. The effect on the radioactivity of the keto acids of an additional period intracer-free air, with and without light, as well as the dark incorporation of C14O2 was studied. These results are discussed in relation to the role of the ketoacids in photosynthesis. It is concluded that the synthesis of amino acids such as glycine, serine, and aspartic acid may be effected by mechanisms other than transamination in green leaves in the light.


Author(s):  
I. P. Wright ◽  
S. Sheridan ◽  
G. H. Morgan ◽  
S. J. Barber ◽  
A. D. Morse

The Ptolemy instrument on the Philae lander (of the Rosetta space mission) was able to make measurements of the major volatiles, water, carbon monoxide and carbon dioxide, directly at the surface of comet 67P/Churyumov–Gerasimenko. We give some background to the mission and highlight those instruments that have already given insights into the notion of water in comets, and which will continue to do so as more results are either acquired or more fully interpreted. On the basis of our results, we show how comets may in fact be heterogeneous over their surface, and how surface measurements can be used in a quest to comprehend the daily cycles of processes that affect the evolution of comets. This article is part of the themed issue ‘The origin, history and role of water in the evolution of the inner Solar System’.


1969 ◽  
Vol 111 (4) ◽  
pp. 537-545 ◽  
Author(s):  
A. R. Hunter ◽  
L. S. Jefferson

1. By perfusion of rat livers with 3mm-AMP in the perfusion medium we obtain increased intracellular concentrations of AMP. 2. These high intracellular concentrations of AMP lead to an increased output of glucose and urea into the perfusion medium. 3. The increased output of glucose in livers from fed rats is brought about primarily by an AMP-stimulated breakdown of liver glycogen. In livers from starved rats the increase in glucose output is not as great, reflecting the low contents of glycogen in livers from starved rats. 4. AMP inhibits gluconeogenesis from lactate in perfused livers. In the presence of high concentrations of lactate, however, the counteracting effects of AMP to increase glycogenolysis and to inhibit gluconeogenesis result in little change in the net glucose output. 5. The increased urea output is brought about by increased breakdown of amino acids that are present in the perfusion medium. In livers from starved rats the overall urea production is much higher, indicating increased catabolism of amino acids and other nitrogenous substrates in the absence of carbohydrate substrates. 6. AMP causes an inhibition of incorporation of labelled precursors into protein and nucleic acid. This may result from increased catabolism of precursors of proteins and nucleic acids as reflected by the more rapid breakdown of nitrogenous compounds. In support of this hypothesis, cell-free systems for amino acid incorporation isolated from livers perfused with and without AMP are equally capable of supporting protein synthesis. 7. The labelling pattern of RNA in perfused livers corresponds very closely to those found by pulse-labelling in vivo. AMP in no way alters the qualitative nature of the labelling patterns. 8. We consider these results as supporting evidence for the role of the concentration ratio of AMP to ATP in controlling the metabolic pathways that lead to the formation of ATP.


2021 ◽  
Author(s):  
◽  
Oliver Bone

<p>Cnidarian-dinoflagellate symbioses occur across a wide latitudinal range, from temperate to tropical locations in both hemispheres. In the tropics, this association provides the foundation for the development of highly diverse coral reef ecosystems. Tropical associations are particularly sensitive to thermal variability, however, leading to dysfunction of the relationship and eventual expulsion of the symbiont, known as ‘coral bleaching’. In contrast, temperate associations maintain stable symbiotic relationships in highly fluctuating thermal environments. The reason behind the relative thermal tolerance of temperate associations is still unclear, though the ability to maintain cellular homeostasis through adjustments to metabolic processes is likely a core feature of their resilience.  Both a field study and laboratory experiment were conducted to determine the metabolic responses to thermal change of the symbiosis between the temperate anemone Anthopleura aureoradiata and the dinoflagellate Symbiodinium. For the field component, A. aureoradiata were collected from Point Halswell in Wellington Harbour in both summer and winter. For the laboratory experiment, specimens collected at Pautahanui inlet were thermally acclimated in the laboratory, after which temperatures were altered over the course of one week to either 8°C (cold) or 28°C (hot) and maintained at these temperatures for six weeks. Gas chromatography coupled to mass spectrometry was then employed to determine the identity and relative quantity of a wide range of metabolites involved in primary metabolism including organic acids, fatty acids, amino acids and sugars. Based on these data, pathway activity profiling was used to determine the activity of different metabolic pathways both between seasons and in response to cold and heat treatment.  A wide range of changes to metabolic processes were observed in both host and symbiont. Photosynthetic capacity was reduced in the symbionts at low temperatures and increased at high temperatures. The only organic acid to be significantly impacted was propanedioic acid, which increased in the host in response to cold treatment, potentially related to increased translocation from the symbiont. Altered fatty acid content in both host and symbiont was related to the role of fatty acids as energy sources and storage compounds and in cell signalling processes. Changes in fatty acid-associated metabolic pathways were exemplified by arachidonic acid and linoleic acid metabolism. Alterations to free amino acids and amino acid related pathways in both host and symbiont were associated with their role as antioxidants and osmoprotectants and the catabolism of amino acids for the production of energy. In symbionts only, altered amino acid content was associated with the role of amino acids in the production of alkaloids. Changes in a number of sugar derivatives in both host and symbiont were associated with their role as antioxidants and osmoprotectants. Altered sugar metabolism in the symbiont clearly indicated an increase in the production of energy rich sugar molecules and production of cellular energy in summer/hot conditions and a decrease in winter/cold conditions. Notably impacted pathways included the Calvin cycle, glycolysis, the pentose phosphate pathway and oxidative phosphorylation. Patterns of sugar related pathway activity in the host were generally opposite to that observed in the symbiont. Overall, prominent but opposing changes in the host and symbiont were detected in the central carbohydrate and energy metabolic pathways. In general, the activity of these pathways increased in the host in winter/cold conditions and decreased in summer/hot conditions, while in the symbiont the pattern was the opposite.  These findings highlight the role of metabolic processes in enabling the persistence of a temperate cnidarian-dinoflagellate symbiosis in the face of large temperature fluctuations. This work provides a foundation upon which a deeper understanding of metabolic functioning in the cnidarian-dinoflagellate symbiosis can be built and provides a comparative platform for studies of the more thermally sensitive tropical associations.</p>


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