Resource conservation manifests in the genetic code

Abstract

9Ocean microbes are responsible for about 50% of primary production on Earth, and are strongly 10 affected by environmental resource availability. However, selective forces resulting from 11 environmental conditions are not well understood. We studied selection by examining single-12 nucleotide variants in the marine environment, and discovered strong purifying selective forces 13 exerted across marine microbial genes. We present evidence indicating that this selection is 14 driven by the environment, and especially by nitrogen availability. We further corroborate that 15 nutrient availability drives this 'resource-driven' selection by showing stronger selection on highly 16 expressed and extracellular genes, that are more resource-consuming. Finally, we show that the 17 standard genetic code, along with amino acid abundances, facilitates nutrient conservation by 18 providing robustness to mutations that increase nitrogen and carbon consumption. Notably, this 19 robustness generalizes to multiple taxa across all domains of life, including the Human genome, 20 and manifests in the code structure itself. Overall, we uncover overwhelmingly strong purifying 21 selective pressure across marine microbial life that may have contributed to the structure of our 22 genetic code. 23 could be attributed to the different rates of synonymous mutations between the high-and low-595 nitrate groups, which, combined with simplex properties, may affect observed nonsynonymous

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

“…Genomic DNA with high GC content is considered to be more thermostable 34 , yet incurs a higher biochemical cost compared with AT base synthesis 35 . It has been shown that nutrient limitation provides a strong selection pressure on nucleotide usage in prokaryotes 36 and plants 37 leading to a bias towards ATrich genomes. Thus, it is possible that the long-term deamination of methylated cytosine residues, and a reduction in genome size after the ancestral WGD event, would have resulted in a more streamlined, water and nutrient-efficient genome (especially given the nutrient costs needed for high levels of methylation silencing, above) that is better adapted to harsh, nutrient-and water-limited conditions.…”

“…High levels of cytosine methylation over millions of years would, in turn, have increased the frequency of deamination of methylated cytosines towards thymine 31,78 , leading to Welwitschia's GC-poor genome. Interestingly, a GC-poor genome may also confer selective advantages under the nutrient stress of Welwitschia's environment, as observed in other plants and bacteria 36,37 , because GC dinucleotides are less N demanding than AT dinucleotides.…”

Metabolic resilience is encoded in genome plasticity

“…A process optimized by evolution through the selection of protein residues favouring multi-molecular assemblies (8,18). This is in line with resource-driven selection, where preservation of energy during nutritional limitation acts as a selective pressure for evolutionary adaptations (19). This selection is also encoded in genomic-rearrangements or cis-regulatory substitutions (20) (also known as human accelerated regions, HARs), and 3D optimization of chromatin interactions (21).…”

Nitrogen availability drives gene length of dominant prokaryotes and diversity of genes acquiring Nitrogen-species in oceanic systems

“…The copyright holder for this this version posted January 10, 2021. ; https://doi.org/10.1101/2021.01.10.426031 doi: bioRxiv preprint virus families of the AOM implies that N-availability or coupled growth constraints such as energy limitation drive the adaptive reduction in gene length with decreasing N-concentration. Hence, Nlimitation appears to affect not only genome size, purifying selection towards a reduced genomic G+C content and N-ARSC of many marine bacterial genera [8][9][10] but also AGL thus further lowering the N-demand and energy costs of biosynthetic reactions and DNA-replication. To compare the effect of saving N by reducing AGL, G+C content or N-ARSC we analyzed the theoretically reduced demand of N atoms required for nucleotides and amino acids as a function of transcription and translation cycles for these three variables in observed ranges occurring in marine prokaryotes (see above, Fig.…”

“…Despite this general trend, under strong environmental constraints genome size, the genomic G+C content, and purifying selection towards a reduced genomic N-content of prokaryotes underlies selective forces leading to a reduced G+C content and genome size to utilize limiting resources more efficiently. A consistently low ratio of nonsynonymous polymorphisms to synonymous polymorphisms in the Tara Ocean prokaryotic gene set and the identification of nitrate as the strongest environmental variable correlating with this ratio indicates that purifying selection drives the reduced genomic N-content of oceanic prokaryotes 8 . The relatively low G+C content and small genomes of bacterial lineages in stratified oceans, in particular the abundant cyanobacterium Prochlorococcus, the alphaproteobacterial Pelagibacteraceae/SAR11 and the gammaproteobacterial SAR86 clades, are the result of genome streamlining 2 and strong N-limitation 4,9 because the nucleobases G+C require one atom more N than A+T.…”