The genetic code is not optimized for resource conservation

Xu, Haiqing; Zhang, J

doi:10.1101/2021.02.08.430341

Cited by 2 publications

(2 citation statements)

References 12 publications

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“…This simple fact makes it difficult to justify the ERMC as a measure of the cost of missense mutations, because it only accounts for increases. Indeed, contemporaneous work to ours shows that the SGC is not optimized for resource conservation when the ERMC is modified to also account for decreases in the number of nitrogen or carbon atoms ( Xu and Zhang 2021b ). Taken together, our analyses strongly suggest that the SGC is not optimized for resource conservation.…”

Section: Discussionmentioning

confidence: 97%

Little Evidence the Standard Genetic Code Is Optimized for Resource Conservation

Rozhoňová

Payne

2021

Molecular Biology and Evolution

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Selection for resource conservation can shape the coding sequences of organisms living in nutrient-limited environments. Recently, it was proposed that selection for resource conservation, specifically for nitrogen and carbon content, has also shaped the structure of the standard genetic code, such that the missense mutations the code allows tend to cause small increases in the number of nitrogen and carbon atoms in amino acids. Moreover, it was proposed that this optimization is not confounded by known optimizations of the standard genetic code, such as for polar requirement or hydropathy. We challenge these claims. We show the proposed optimization for nitrogen conservation is highly sensitive to choice of null model and the proposed optimization for carbon conservation is confounded by the known conservative nature of the standard genetic code with respect to the molecular volume of amino acids. There is therefore little evidence the standard genetic code is optimized for resource conservation. We discuss our findings in the context of null models of the standard genetic code.

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Section: Discussionmentioning

confidence: 97%

Little Evidence the Standard Genetic Code Is Optimized for Resource Conservation

Rozhoňová

Payne

2021

Molecular Biology and Evolution

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“…It is important to note that some other putatively optimal properties have been shown to not be independently optimal and thus are perhaps an artefact of already-known facets of code structure. In addition to the putative frameshift optimality addressed above (Xu and Zhang 2021a), a prominent study in Science claimed that the code is near optimal for resource conservation (Shenhav and Zeevi 2020), but this claim has been subjected to rigorous critique in two response papers (Rozhoñová and Payne 2021; Xu and Zhang 2021b). The idea that the structure of the code may be a result of selection in general remains controversial (Massey 2008, 2016; Di Giulio 2018; Wichmann and Ardern 2019), but optimality is a distinct question from that of historical process.…”

Section: Discussionmentioning

confidence: 99%

Why is the average collateral effect of synonymous mutations so similar across alternative reading frames?

Wichmann

Ardern

2022

Preprint

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The standard genetic code has been shown to have multiple interesting properties which impact on molecular biology and the evolutionary process. One facet of molecular biology where code structure is particularly important is the origin and evolution of overlapping genes. We have previously reported that the structure of the standard genetic code ensures that synonymous mutations in a protein coding gene will lead to a remarkably similar average "collateral" mutation effect size in at least four out of the five alternative reading frames. Here we show that only 0.26% of alternative codes with the block structure of the standard genetic code perform at least as well as the standard code in this property. Considering this finding within a code optimality framework suggests that this consistent effect size across the different frames may be adaptive. Here we give context for this finding and present a simple model where a trade-off between evolvability and robustness leads to an average mutation effect size which maximises population fitness. This supports the intuition that similar mutation effects across the different alternative reading frames may be an adaptive property of the standard genetic code which facilitates evolvability through the use of alternative reading frames.

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The genetic code is not optimized for resource conservation

Cited by 2 publications

References 12 publications

Little Evidence the Standard Genetic Code Is Optimized for Resource Conservation

Little Evidence the Standard Genetic Code Is Optimized for Resource Conservation

Why is the average collateral effect of synonymous mutations so similar across alternative reading frames?

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