The structure–function analysis of Obg‐like <scp>GTPase</scp> proteins along the evolutionary tree from bacteria to humans

Chakraborty, Asmita; Halder, Sheta; Kishore, Purvi; Saha, Disha; Saha, Sujata; Sikder, Kunal; Basu, Arnab

doi:10.1111/gtc.12942

Cited by 9 publications

(3 citation statements)

References 67 publications

(121 reference statements)

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“…Members of the Obg subfamily of G-proteins, and the E. coli representative ObgE in particular, function at the crossroads of a large plethora of cellular functions, including ribosome assembly/maturation, DNA replication, cell division, stress response and persistence ( 6 , 10 ). Based on this wide variety of functional roles one would expect that ObgE acts as a cellular hub that interacts with a large set of regulatory proteins and downstream effectors.…”

Section: Discussionmentioning

confidence: 99%

YbiB: a novel interactor of the GTPase ObgE

Deckers

Vercauteren

Kock

et al. 2023

Nucleic Acids Research

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Obg is a widely conserved and essential GTPase in bacteria, which plays a central role in a large range of important cellular processes, such as ribosome biogenesis, DNA replication, cell division and bacterial persistence. Nevertheless, the exact function of Obg in these processes and the interactions it makes within the associated pathways remain largely unknown. Here, we identify the DNA-binding TrpD2 protein YbiB as an interactor of the Escherichia coli Obg (ObgE). We show that both proteins interact with high affinity in a peculiar biphasic fashion, and pinpoint the intrinsically disordered and highly negatively charged C-terminal domain of ObgE as a main driver for this interaction. Molecular docking and X-ray crystallography, together with site-directed mutagenesis, are used to map the binding site of this ObgE C-terminal domain within a highly positively charged groove on the surface of the YbiB homodimer. Correspondingly, ObgE efficiently inhibits the binding of DNA to YbiB, indicating that ObgE competes with DNA for binding in the positive clefts of YbiB. This study thus forms an important step for the further elucidation of the interactome and cellular role of the essential bacterial protein Obg.

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Section: Discussionmentioning

confidence: 99%

YbiB: a novel interactor of the GTPase ObgE

Deckers

Vercauteren

Kock

et al. 2023

Nucleic Acids Research

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“…The 9 methyltransferases that might be involved in the fine tuning of ribosomal decoding center [62] include 4 putative tRNA/rRNA methyltransferases of the SpoU family (SCO3836, SCO1552, SCO1597 and SCO4236) [63], 4 methyl transferases of the small subunit of the rRNA: RsmC-like (SCO1041) [64], RsmE-like (SCO2552) [65], RsmH-like (SCO2092) [66] and RsmI-like (SCO3253) [67] as well as a rRNA adenine dimethylase of the KsgA family (SCO3149) [68]. The 3 GTPases involved in ribosome assembly and homeostasis [69] belong to the Era (SCO2539) [70], Der/EngA (SCO1758) [71] or Obg (SCO2595) [72] families. Interestingly, in condition of over-expression Obg has a negative impact on aerial mycelium formation in SC [73].…”

Section: Otherwise This Group Includes 9 Methyltransferases [55]mentioning

confidence: 99%

The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor

Lejeune,

Cornu,

Sago

et al. 2024

Research in Microbiology

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“…In many biological and animal models, the bacterial mutants that cannot produce ppGpp usually show a reduced ability of persister formation [ 25 , 43 , 44 , 45 ]. In the stationary phase, the elevated recruitment of ppGpp to Obg GTPase results in the excessive binding of Obg to the 50S ribosome subunit, which reduces the levels of active 70S ribosomes and thereby regulates cellular functions and participates in various stress adaptions like the stringent response [ 32 , 46 ]. In persisters, Obg induces the expression of HokB, a membrane-targeted type I toxin, which can damage proton motion and block ATP synthesis, leading to dormancy [ 32 ].…”

Section: Research On the Mechanism Of Bacterial Persistencementioning

confidence: 99%

Recent Advances in Bacterial Persistence Mechanisms

Pan,

Liu,

et al. 2023

IJMS

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The recurrence of bacterial infectious diseases is closely associated with bacterial persisters. This subpopulation of bacteria can escape antibiotic treatment by entering a metabolic status of low activity through various mechanisms, for example, biofilm, toxin–antitoxin modules, the stringent response, and the SOS response. Correspondingly, multiple new treatments are being developed. However, due to their spontaneous low abundance in populations and the lack of research on in vivo interactions between persisters and the host’s immune system, microfluidics, high-throughput sequencing, and microscopy techniques are combined innovatively to explore the mechanisms of persister formation and maintenance at the single-cell level. Here, we outline the main mechanisms of persister formation, and describe the cutting-edge technology for further research. Despite the significant progress regarding study techniques, some challenges remain to be tackled.

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The structure–function analysis of Obg‐like GTPase proteins along the evolutionary tree from bacteria to humans

Cited by 9 publications

References 67 publications

YbiB: a novel interactor of the GTPase ObgE

YbiB: a novel interactor of the GTPase ObgE

The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor

Recent Advances in Bacterial Persistence Mechanisms

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