The hypothesized role of YbeZ in 16S rRNA maturation

Andrews, Emma S.V.; Patrick, Wayne M.

doi:10.1007/s00203-021-02739-z

Cited by 3 publications

(3 citation statements)

References 28 publications

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“…Looking at era syntenies across multiple model species, one can single out a few genes that pop up time and again next to era or in its close proximity ( Figure 1B ). Thus, in many Terrabacteria, era is adjacent to genes encoding the ribosome assembly factor YbeY and its highly conserved partner YbeZ/PhoH-like, involved in the biogenesis of the platform and the 3′-domain of 16S rRNA ( Liao et al, 2021 ; Andrews and Patrick, 2022 ). Three other genes associated with ribosome biogenesis and frequently found close to era are rnc, rsmE, and lepA .…”

Section: Evolutionary Journey Of Era Gtpasesmentioning

confidence: 99%

GTPase Era at the heart of ribosome assembly

Gruffaz,

Smirnov

2023

Front. Mol. Biosci.

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Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.

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Section: Evolutionary Journey Of Era Gtpasesmentioning

confidence: 99%

GTPase Era at the heart of ribosome assembly

Gruffaz,

Smirnov

2023

Front. Mol. Biosci.

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“…ybeZ encodes a phosphate starvation‐regulated PhoH subfamily protein with the NTP hydrolase domain (Kim et al., 1993). YbeZ has phosphatase activity and is a putative RNA helicase through sequence homology (Andrews & Patrick, 2022; Kazakov et al., 2003). A physical interaction between YbeY and YbeZ was suggested based on bacterial two‐hybrid system experiments in E. coli (Vercruysse et al., 2016).…”

Section: Introductionmentioning

confidence: 99%

Involvement of Escherichia coli YbeX/CorC in ribosomal metabolism

Sarıgül,

Žukova,

Alparslan

et al. 2024

Molecular Microbiology

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YbeX of Escherichia coli, a member of the CorC protein family, is encoded in the same operon with ribosome‐associated proteins YbeY and YbeZ. Here, we report the involvement of YbeX in ribosomal metabolism. The ΔybeX cells accumulate distinct 16S rRNA degradation intermediates in the 30S particles and the 70S ribosomes. E. coli lacking ybeX has a lengthened lag phase upon outgrowth from the stationary phase. This growth phenotype is heterogeneous at the individual cell level and especially prominent under low extracellular magnesium levels. The ΔybeX strain is sensitive to elevated growth temperatures and to several ribosome‐targeting antibiotics that have in common the ability to induce the cold shock response in E. coli. Although generally milder, the phenotypes of the ΔybeX mutant overlap with those caused by ybeY deletion. A genetic screen revealed partial compensation of the ΔybeX growth phenotype by the overexpression of YbeY. These findings indicate an interconnectedness among the ybeZYX operon genes, highlighting their roles in ribosomal assembly and/or degradation.

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“…ybeZ encodes a phosphate starvation-regulated PhoH subfamily protein with the NTP hydrolase domain (Kim et al ., 1993). YbeZ has phosphatase activity and is a putative RNA helicase through sequence homology (Kazakov et al ., 2003; Andrews and Patrick, 2022). A physical interaction between YbeY and YbeZ was suggested based on bacterial two-hybrid system experiments in E. coli (Vercruysse et al ., 2016).…”

Section: Introductionmentioning

confidence: 99%

Involvement of the putative metal efflux protein YbeX in ribosomal metabolism

Sarigül

Žukova

Alparslan

et al. 2023

Preprint

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YbeX ofEscherichia coli, a member of CorC protein family, is a putative Co2+/ Mg2+efflux factor. Here, we describe severalΔybeXphenotypes and report an involvement of YbeX in ribosomal metabolism.E. colilackingybeXhas a longer lag phase on outgrowth from the stationary phase. This phenotype is heterogeneous at the individual cell level and can be rescued by supplementing the growth media with magnesium.ΔybeXstrain is sensitive to elevated growth temperatures and to several ribosome-targeting antibiotics, which have a common ability to induce the cold shock response inE. coli.ΔybeXcells accumulate distinct 16S rRNA degradation intermediates present in both 30S particles and 70S ribosomes. We propose that a function of YbeX is maintaining the magnesium homeostasis in the cell, which is needed for proper ribosomal assembly.

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The hypothesized role of YbeZ in 16S rRNA maturation

Cited by 3 publications

References 28 publications

GTPase Era at the heart of ribosome assembly

GTPase Era at the heart of ribosome assembly

Involvement of Escherichia coli YbeX/CorC in ribosomal metabolism

Involvement of the putative metal efflux protein YbeX in ribosomal metabolism

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