scholarly journals Resource conservation manifests in the genetic code

Science ◽  
2020 ◽  
Vol 370 (6517) ◽  
pp. 683-687
Author(s):  
Liat Shenhav ◽  
David Zeevi
Keyword(s):  
Genetic Code ◽  
Nutrient Limitation ◽  
Nitrogen Availability ◽  
Resource Conservation ◽  
Marine Microbes ◽  
Carbon And Nitrogen ◽  
Selective Pressures ◽  
Domains Of Life ◽  
Cell Data ◽  
Competition For Resources

Nutrient limitation drives competition for resources across organisms. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this “resource-driven selection” by using metagenomic and single-cell data of marine microbes, alongside environmental measurements. We show that a significant portion of the selection exerted on microbes is explained by the environment and is associated with nitrogen availability. Notably, this resource conservation optimization is encoded in the structure of the standard genetic code, providing robustness against mutations that increase carbon and nitrogen incorporation into protein sequences. This robustness generalizes to codon choices from multiple taxa across all domains of life, including the human genome.

scholarly journals Resource conservation manifests in the genetic code

2019 ◽  
Author(s):  
Liat Shenhav ◽  
David Zeevi
Keyword(s):  
Genetic Code ◽  
Nutrient Limitation ◽  
Nitrogen Availability ◽  
Resource Conservation ◽  
Marine Microbes ◽  
Coding Sequences ◽  
Carbon And Nitrogen ◽  
Nutrient Conservation ◽  
Cell Data ◽  
Competition For Resources

AbstractNutrient limitation is a strong selective force, driving competition for resources. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this ‘resource-driven’ selection using metagenomic and single-cell data of marine microbes, alongside environmental measurements. We show that a significant portion of the selection exerted on microbes is explained by the environment and is strongly associated with nitrogen availability. We further demonstrate that this resource conservation optimization is encoded in the structure of the standard genetic code, providing robustness against mutations that increase carbon and nitrogen incorporation into protein sequences. Overall, we demonstrate that nutrient conservation exerts a significant selective pressure on coding sequences and may have even contributed to the evolution of the genetic code.

scholarly journals Improved Eco-Friendly RecombinantAnabaenasp. Strain PCC7120 with Enhanced Nitrogen Biofertilizer Potential

2010 ◽  
Vol 77 (2) ◽  
pp. 395-399 ◽  
Author(s):  
Akhilesh Kumar Chaurasia ◽  
Shree Kumar Apte
Keyword(s):  
Recombinant Strain ◽  
Nitrogen Availability ◽  
Nitrogenase Activity ◽  
Inducible Promoter ◽  
Paddy Fields ◽  
Environmental Application ◽  
Carbon And Nitrogen ◽  
Enhanced Expression ◽  
Photosynthesis And Respiration ◽  
Nitrogen Demand

ABSTRACTPhotosynthetic, nitrogen-fixingAnabaenastrains are native to tropical paddy fields and contribute to the carbon and nitrogen economy of such soils. Genetic engineering was employed to improve the nitrogen biofertilizer potential ofAnabaenasp. strain PCC7120. Constitutive enhanced expression of an additional integrated copy of thehetRgene from a light-inducible promoter elevated HetR protein expression and enhanced functional heterocyst frequency in the recombinant strain. The recombinant strain displayed consistently higher nitrogenase activity than the wild-type strain and appeared to be in homeostasis with compatible modulation of photosynthesis and respiration. The enhanced combined nitrogen availability from the recombinant strain positively catered to the nitrogen demand of rice seedlings in short-term hydroponic experiments and supported better growth. The engineered strain is stable, eco-friendly, and useful for environmental application as nitrogen biofertilizer in paddy fields.

Water table and species identity outweigh carbon and nitrogen availability in a softwater plant community

2013 ◽  
Vol 47 ◽  
pp. 57-67 ◽  
Author(s):  
Floris Vanderhaeghe ◽  
Alfons J.P. Smolders ◽  
Jan G.M. Roelofs ◽  
Maurice Hoffmann
Keyword(s):  
Plant Community ◽  
Water Table ◽  
Nitrogen Availability ◽  
Species Identity ◽  
Carbon And Nitrogen ◽  
Carbon And Nitrogen Availability

scholarly journals The non-power model of the genetic code: a paradigm for interpreting genomic information

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150062 ◽  
Author(s):  
Diego Luis Gonzalez ◽  
Simone Giannerini ◽  
Rodolfo Rosa
Keyword(s):  
Genetic Code ◽  
Power Model ◽  
Mathematical Framework ◽  
Genomic Information ◽  
Unified Framework ◽  
Hidden Symmetries ◽  
Protein Coding ◽  
The Core ◽  
Domains Of Life ◽  
Mitochondrial Code

In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications.

scholarly journals The genetic code is not optimized for resource conservation

2021 ◽  
Author(s):  
Haiqing Xu ◽  
Jianzhi Zhang
Keyword(s):  
Genetic Code ◽  
Recent Article ◽  
Resource Conservation ◽  
Universal Genetic Code ◽  
Genetic Codes

AbstractShenhav and Zeevi conclude in a recent article (Science 370:683-687) that the universal genetic code (UGC) is optimized for resource conservation because mutations are less likely to increase proteomic nitrogen and carbon uses under the UGC than under random genetic codes (RGCs). Their finding results from miscalculating mutational effects and benchmarking against biased RGCs. Our reanalysis refutes their conclusion.

On the Relationships between the Genetic Code Coevolution Hypothesis and the Physicochemical Hypothesis

1991 ◽  
Vol 46 (3-4) ◽  
pp. 305-312 ◽  
Author(s):  
Massimo Di Giulio
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Comparative Study ◽  
Genetic Code ◽  
Selective Pressure ◽  
Active Role ◽  
Selective Pressures ◽  
Evolutionary Hypothesis

This paper analyzes the relationships between the genetic code coevolution hypothesis and the physicochemical hypothesis by means of a comparative study of the precursor-product amino acid pairs on which the former hypothesis is based. Even if the coevolution between the biosynthetic relationships of amino acids and the organization of the genetic code is not questioned in this paper, the results and the arguments used lead us to believe that the selective pressures considered essential by the physicochemical postulates, played a more active role than that of the precursor-product relationships in defining the allocation of these amino acids in the genetic code. It is furthermore pointed out that the two evolutionary hypothesis might be aspects of the same selective pressure, and thus difficult to differentiate.

Disentangling the long-term foliar 15N signal using a land surface model

2020 ◽  
Author(s):  
Silvia Caldararu ◽  
Tea Thum ◽  
Richard Nair ◽  
Sönke Zaehle
Keyword(s):  
Nutrient Limitation ◽  
Land Surface ◽  
Nitrogen Availability ◽  
Land Surface Model ◽  
Ecosystem Dynamics ◽  
Surface Model ◽  
Terrestrial Vegetation ◽  
Climate System Model ◽  
Foliar N

<p>Terrestrial vegetation growth is hypothesised to increase under elevated atmospheric CO<sub>2</sub>, a process known as the CO<sub>2</sub> fertilisation effect. However, the magnitude of this effect and its long-term sustainability remains uncertain. One of the main limitations to the CO2  fertilisation effect is nutrient limitation to plant growth, in particular nitrogen (N) in temperate and boreal ecosystems. Recent studies have suggested that decreases in observed foliar N content (N%) and δ<sup>15</sup>N indicate widespread nitrogen limitation with increasing CO<sub>2</sub>  concentrations. However, the factors driving these two variables, and especially the foliar δ<sup>15</sup>N values, are complex and can be caused by a number of processes. On one hand, if the observed trends reflect nutrient limitation, this limitation can be caused by either CO<sub>2</sub> or warming driven growth. On the other hand, it is possible that nutrient limitation does not occur to its full extent due to plant plastic responses to alleviate nutrient limitation, causing a decrease in N%, but changes in the anthropogenic N deposition 15N signal cause the observed δ<sup>15</sup>N trend. In reality, it is likely that all these factors contribute to the observed trends. To understand ecosystem dynamics it is important to disentangle the processes behind these signals which is very difficult based on observational datasets only.</p><p>We use a novel land surface model to explore the causes behind the observed trends in foliar N% and δ<sup>15</sup>N. The QUINCY (QUantifying Interactions between terrestrial Nutrient CYcles and the climate system) model  has the unique capacity to track ecologically relevant isotopic composition, including <sup>15</sup>N in plant and soil pools. The model also includes a realistic representation of plant plastic acclimation processes, specifically a representation of nitrogen allocation to and inside the canopy in response to nitrogen availability, so implicitly to changes in CO<sub>2 </sub> concentrations. We test the different hypotheses above behind the observed changes in N% and δ<sup>15</sup>N separately and quantify the contribution of each of the factors towards the observed trend. We then test the different hypotheses against existing observations of N% and δ<sup>15</sup>N from the ICP Forests database and other published datasets such as the global dataset of Craine et al. 2018.</p><p>Our study showcases the use of an isotope-enabled land surface model in conjunction with long-term observations to strengthen our understanding of the ecosystem processes behind the observed trends.</p>

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