Why Nature Chose Potassium

Danchin, Antoine; Nikel, Pablo I.

doi:10.1007/s00239-019-09915-2

Cited by 44 publications

(44 citation statements)

References 189 publications

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“…This implies that the MnmEG complex must discriminate against a variety of uridine residues located within RNA loops. This discrimination is performed by the potassium‐dependent GTPase activity of subunit E of the complex (Fislage et al , 2016; Shalaeva et al , 2018; Boel et al , 2019; Danchin and Nikel, 2019; Gao et al , 2019). Remarkably, this subunit also regulates the activity of the H 4 F‐related enzyme, poly‐γ‐glutamyl H 2 F/H 4 F synthase FolC, discussed at the beginning of this article.…”

Section: Folate‐dependent Modification Of Rnas and Proteinsmentioning

confidence: 99%

One‐carbon metabolism, folate, zinc and translation

Danchin

Sekowska

You

2020

Microbial Biotechnology

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The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells.Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.

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Section: Folate‐dependent Modification Of Rnas and Proteinsmentioning

confidence: 99%

One‐carbon metabolism, folate, zinc and translation

Danchin

Sekowska

You

2020

Microbial Biotechnology

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“…Some examples are iridium, [225] ruthenium, [226] palladium, [227] osmium [228] and rhodium. [229] Although the incorporation of metallic elements into living cells by neometabolism awaits further development, critically revisiting the role of alkali metallic ions (e. g., potassium, [230] widespread in life) indicates that they have been selected because of some of their idiosyncratic properties rather than by an accidental evolutionary occurrence. These principles provide fundamental guidance towards engineering routes for integration of nonbiological atoms into the biochemistry of microbial cells.…”

Section: Metallic Elementsmentioning

confidence: 99%

Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life

Nieto-Domínguez

Nikel

2020

ChemBioChem

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The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism – yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno‐elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new‐to‐nature molecules, such as organohalides.

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“…The small difference in the nature of binding between Na + and K + may be responsible for the difference in their effects on the higher-order structure of DNA, through competitions of large number of monovalent cations, Na + /K + , with number of SPD molecules for DNA binding. If we consider DNA of around the size of 100kbp, as in Figs 2 and 3, the number of negative phosphate groups is around 2�10 5 . This indicates that the small difference in the nature of binding of Na + and K + may induce a large difference in the higher-order structural change through the binding of SPD to the larger number of available phosphate groups.…”

Section: Plos Onementioning

confidence: 99%

K+ promotes the favorable effect of polyamine on gene expression better than Na+

et al. 2020

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Background Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K + enhanced in vitro gene expression in the presence of polyamine more strongly than Na +. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K + and Na +. Principal findings It was found that K + enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na + , through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na + prevents the folding transition of DNA into a compact state more strongly than K +. 1 H NMR measurement revealed that Na + inhibits the binding of SPD to DNA more strongly than K +. Thus, SPD binds to DNA more favorably in K +-rich medium than in Na +-rich medium, which leads to favorable conditions for RNA polymerase to access DNA by decreasing the negative charge. Conclusion and significance We found that Na + and K + exhibit markedly different effects through competitive binding with a cationic polyamine, SPD, to DNA, which causes a large difference in the higher-order structure of genomic DNA. It is concluded that the larger favorable effect of Na + than K + on in vitro gene expression observed in this study is well attributable to the significant difference between Na + and K + on the competitive binding inducing conformational transition of DNA.

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Why Nature Chose Potassium

Cited by 44 publications

References 189 publications

One‐carbon metabolism, folate, zinc and translation

One‐carbon metabolism, folate, zinc and translation

Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life

K+ promotes the favorable effect of polyamine on gene expression better than Na+

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