The genetic law of the minimum

doi:10.1126/science.abf2588

GSTDTAP > 气候变化

DOI	10.1126/science.abf2588
	The genetic law of the minimum
	Martin F. Polz; Otto X. Cordero
	2020-11-06
发表期刊	Science
出版年	2020
英文摘要	How organisms are optimized in the face of environmental challenges remains one of the key unanswered questions in biology. The optimization of enzymes for changing nutrient concentrations in an organism's environment is well known ([ 1 ][1]). However, intricate genomics studies have revealed that optimization might affect the architecture of the entire genome ([ 2 ][2]). On page 683 of this issue, Shenhav and Zeevi ([ 3 ][3]) illuminate how selection driven by resource scarcity can affect the evolution of nucleotide and protein sequences in marine microbes. In extremely nutrient-scarce regions of the ocean, microbial genomes are often small and streamlined, containing only the most essential genetic information ([ 4 ][4]). However, the essential selective factor often is not the absolute concentration of a single nutrient but rather its ratio with other required nutrients ([ 5 ][5]). For example, the sunlit ocean surface is typically limited in nitrogen but not organic carbon, because photosynthetic organisms require much of the former but produce copious amounts of the latter. When biomass from this surface layer dies and sinks, it is degraded by heterotrophic bacteria, which, because of the stoichiometry of elements in their food versus their cells, shift the balance toward carbon limitation ([ 6 ][6], [ 7 ][7]). Recent work has shown that this transition from nitrogen to carbon limitation provides an explanation for an abrupt shift in the guanine-cytosine (GC) content in the genomes of marine microbes at the ocean surface versus those in the deep ocean ([ 8 ][8], [ 9 ][9]). Organisms living under consistent nitrogen limitation have a low GC content in their genomes, leading to a lower nitrogen demand for DNA synthesis. These organisms also use codons that favor a proteome with a comparatively low nitrogen and high carbon content ([ 10 ][10], [ 11 ][11]). Using a large set of metagenomic and single-cell genome data from across the global ocean, Shenhav and Zeevi show that natural selection purged nucleotide and amino acid changes that increase the demand for limiting resources. Selection was stronger at the protein versus DNA level, which is consistent with the high protein-to-DNA ratio in microbial cells. Highly expressed and secreted proteins showed the strongest signal for resource-driven selection because they place a high resource demand on the cell. Among the measured environmental variables, nitrate concentration—the prevailing form of nitrogen at the ocean surface ([ 6 ][6])—was most strongly associated with the selection of protein sequences. Furthermore, mutations leading to lower nitrogen incorporation were inversely associated with mutations leading to lower carbon demand. This finding reflects the inverse relationship of carbon and nitrogen limitation as a function of water-column depth. The new insight that carbon limitation might also select for lower carbon incorporation led the authors to link these observations to the nature of the genetic code, which appeared to be simultaneously optimized for conservation of nitrogen and carbon. These findings strengthen the hypothesis that the microbial genome evolved to enable nutrient conservation in low-nitrogen and low-carbon environments. Although variations of the standard genetic code (for example, in mammalian mitochondria or mycoplasma) show that the code itself can evolve, the variants are minor and derived from the standard code shared by all life-forms. Thus, the basic structure of the code, with its characteristic amino acid assignments, is believed to be ancestral to all extant cellular life-forms. Multiple (non–mutually exclusive) theories have been proposed to explain how the code originated ([ 12 ][12]). One of these—the adaptive theory—postulates that the genetic code evolved to maximize mutational robustness (that is, to lower the chance that random mutations lead to deleterious effects caused by translation errors) ([ 13 ][13]). The results of Shenhav and Zeevi add to this theory by showing that the code is also robust in the sense that it minimizes the impact of random mutations on carbon and nitrogen demand. Thus, the code seems to have evolved to minimize the potential damage of random mutations, both in terms of mistranslations and inefficient resource use. This new insight indicates that differential limitation by carbon and nitrogen constrained the evolution of the most primordial forms of life when the universal genetic code evolved. ![Figure][14] Resource use is hardwired in the genome Optimal resource use has been a selective evolutionary force since before the last common ancestor (LCA) diversified into modern life (top). The genetic code evolved to afford marine microbes the ability to adaptively minimize nitrogen (N) or carbon (C) content in their biomass, depending on the nutrient availability in the environment (bottom, ocean). GRAPHIC: KELLIE HOLOSKI/ SCIENCE The findings of Shenhav and Zeevi point to an incredible fine-tuning of genomes toward nutrient availability where selection acts on individual codons. However, whereas single mutations that affect the performance or regulation of proteins can have large fitness effects, the fitness gain of an individual-codon mutation in a protein that optimizes resource use must be vanishingly small. Using, as a reference, the composition of Escherichia coli , a cell with a single nitrogen-saving codon mutation in a highly expressed protein (present at 104 copies per cell), would experience a change in nitrogen demand on the order of only ∼0.001%, assuming ∼109 nitrogen atoms per cell ([ 14 ][15]). With these numbers in mind, it seems hard to imagine a fitness advantage large enough to cause the spread of an adaptive mutation. It would therefore be illuminating to model the effects that such mutations might have on cell physiology and long-term fitness. For example, scientists could develop experimental models of competition experiments under nitrogen limitation to determine whether fitness effects are actually measurable (perhaps as a result of unanticipated pleiotropy). Such experiments could give researchers a better grasp of the magnitude of the relative fitness advantage experienced by the mutant organisms and the evolutionary dynamics that led to the patterns discovered by the authors. The study by Shenhav and Zeevi reveals a fundamental selective force that has affected all forms of cellular life dating back to their last common ancestor and that seems to still be acting today on marine microbes. This work opens many new avenues of inquiry—for example, whether similar patterns of evolution are observed in other environments, such as soils or animal guts; whether mutational patterns of “amino acid choice” can be used to infer resource limitations from metagenomic data; and whether purifying selection acts one amino acid at a time or whether other pleiotropic effects are required to explain the evolution of resource-driven codon selection in microbes. 1. [↵][16]1. B. V. Adkar et al ., Nat. Ecol. Evol. 1, 149 (2017). [OpenUrl][17] 2. [↵][18]1. P. Baudouin-Cornu, 2. Y. Surdin-Kerjan, 3. P. Marlière, 4. D. Thomas , Science 293, 297 (2001). [OpenUrl][19][Abstract/FREE Full Text][20] 3. [↵][21]1. L. Shenhav, 2. D. Zeevi , Science 370, 683 (2020). [OpenUrl][22][Abstract/FREE Full Text][23] 4. [↵][24]1. S. J. Giovannoni, 2. J. C. Thrash, 3. B. Temperton , ISME J. 8, 1553 (2014). [OpenUrl][25][CrossRef][26][PubMed][27] 5. [↵][28]1. K. R. Arrigo , Nature 437, 349 (2005). 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领域	气候变化 ; 资源环境
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引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/301986
专题	气候变化资源环境科学
推荐引用方式 GB/T 7714	Martin F. Polz,Otto X. Cordero. The genetic law of the minimum[J]. Science,2020.
APA	Martin F. Polz,&Otto X. Cordero.(2020).The genetic law of the minimum.Science.
MLA	Martin F. Polz,et al."The genetic law of the minimum".Science (2020).