Invited review: MnmE, a GTPase that drives a complex tRNA modification reaction

Fislage, Marcus; Wauters, Lina; Versées, Wim

doi:10.1002/bip.22813

Cited by 14 publications

(12 citation statements)

References 86 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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“…Another expanding family of G proteins recruits specific cations (such as K ϩ ) to stabilize the GTPase transition state (13)(14)(15)(16). Some G proteins use a combination of the two above strategies, as is the case for MnmE, a G protein involved in tRNA modification (17).…”

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confidence: 99%

Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence

Gkekas

Singh

Shkumatov

et al. 2017

Journal of Biological Chemistry

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The Obg protein family belongs to the TRAFAC (translation factor) class of P-loop GTPases and is conserved from bacteria to eukaryotes. Essential roles in many different cellular processes have been suggested for the Obg protein from (ObgE), and we recently showed that it is a central regulator of bacterial persistence. Here, we report the first crystal structure of ObgE at 1.85-Å resolution in the GDP-bound state, showing the characteristic N-terminal domain and a central G domain that are common to all Obg proteins. ObgE also contains an intrinsically disordered C-terminal domain, and we show here that this domain specifically contributed to GTP binding, whereas it did not influence GDP binding or GTP hydrolysis. Biophysical analysis, using small angle X-ray scattering and multi-angle light scattering experiments, revealed that ObgE is a monomer in solution, regardless of the bound nucleotide. In contrast to recent suggestions, our biochemical analyses further indicate that ObgE is neither activated by K ions nor by homodimerization. However, the ObgE GTPase activity was stimulated upon binding to the ribosome, confirming the ribosome-dependent GTPase activity of the Obg family. Combined, our data represent an important step toward further unraveling the detailed molecular mechanism of ObgE, which might pave the way to further studies into how this GTPase regulates bacterial physiology, including persistence.

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“…AIG-1 is involved in T cell development and survival in animals and in response to biotic and abiotic stress in plants (13). Dynamins are implicated in budding of clathrin coated vesicles from the plasma membrane, mitochondrial division and interferon induced GTPase activity (14) while TrmE proteins are involved in tRNA wobble and uridine modification (15). OBG proteins are postulated to play important roles in many cellular processes like ribosome biogenesis and maturation, chromosome partitioning, DNA replication control (16).…”

Section: Introductionmentioning

confidence: 99%

G-domain prediction across the diversity of G protein families

Sanghavi

Rashmi

Dasgupta

et al. 2019

Preprint

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Guanine nucleotide binding proteins are characterized by a structurally and mechanistically conserved GTP-binding domain, indispensable for binding GTP. The G domain comprises of five adjacent consensus motifs called G boxes, which are separated by amino acid spacers of different lengths. Several G proteins, discovered over time, are characterized by diverse function and sequence. This sequence diversity is also observed in the G box motifs (specifically the G5 box) as well as the inter-G box spacer length. The Spacers and Mismatch Algorithm (SMA) introduced in this study, can predict G-domains in a given G protein sequence, based on user-specified constraints for approximate G-box patterns and inter-box gaps in each G protein family. The SMA parameters can be customized as more G proteins are discovered and characterized structurally. Family-specific G box motifs including the less characterized G5 motif as well as G domain boundaries were predicted with higher precision. Overall, our analysis suggests the possible classification of G protein families based on family-specific G box sequences and lengths of inter-G box spacers. Significance StatementIt is difficult to define the boundaries of a G domain as well as predict G boxes and important GTP-binding residues of a G protein, if structural information is not available. Sequence alignment and phylogenetic methods are often unsuccessful, given the sequence diversity across G protein families. SMA is a unique method which uses approximate pattern matching as well as inter-motif separation constraints to predict the locations of G-boxes. It is able to predict all G boxes including the less characterized G5 motif which marks the carboxy-terminal boundary of a G domain. Thus, SMA can be used to predict G domain boundaries within a large multi-domain protein as long as the user-specified constraints are satisfied. Main Text

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Invited review: MnmE, a GTPase that drives a complex tRNA modification reaction

Cited by 14 publications

References 86 publications

One‐carbon metabolism, folate, zinc and translation

One‐carbon metabolism, folate, zinc and translation

Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence

G-domain prediction across the diversity of G protein families

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