SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli

Singh, Navjot; Bubunenko, Mikhail; Smith, Carol; Abbott, David M.; Stringer, Anne M.; Shi, Ronald; Court, Donald L.; Wade, Joseph T.

doi:10.1128/mbio.00114-16

Cited by 43 publications

(72 citation statements)

References 63 publications

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“…Termination by Rho can be tuned by nascent RNA sequences and trans -acting RNA and protein cofactors that can act directly or indirectly (8, 34, 35). E. coli NusG is the best-characterized activator of Rho.…”

Section: Discussionmentioning

confidence: 99%

A Screen for rfaH Suppressors Reveals a Key Role for a Connector Region of Termination Factor Rho

Artsimovitch

2017

mBio

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RfaH activates horizontally acquired operons that encode lipopolysaccharide core components, pili, toxins, and capsules. Unlike its paralog NusG, which potentiates Rho-mediated silencing, RfaH strongly inhibits Rho. RfaH is recruited to its target operons via a network of contacts with an elongating RNA polymerase (RNAP) and a specific DNA element called ops to modify RNAP into a pause- and NusG-resistant state. rfaH null mutations confer hypersensitivity to antibiotics and detergents, altered susceptibility to bacteriophages, and defects in virulence. Here, we carried out a selection for suppressors that restore the ability of a ΔrfaH mutant Escherichia coli strain to grow in the presence of sodium dodecyl sulfate. We isolated rho, rpoC, and hns suppressor mutants with changes in regions previously shown to be important for their function. In addition, we identified mutants with changes in an unstructured region that connects the primary RNA-binding and helicase domains of Rho. The connector mutants display strong defects in vivo, consistent with their ability to compensate for the loss of RfaH, and act synergistically with bicyclomycin (BCM), which has been recently shown to inhibit Rho transformation into a translocation-competent state. We hypothesize that the flexible connector permits the reorientation of Rho domains and serves as a target for factors that control the motor function of Rho allosterically. Our results, together with the existing data, support a model in which the connector segment plays a hitherto overlooked role in the regulation of Rho-dependent termination.

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Section: Discussionmentioning

confidence: 99%

A Screen for rfaH Suppressors Reveals a Key Role for a Connector Region of Termination Factor Rho

Artsimovitch

2017

mBio

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“…Although classified as a phosphate mobilization gene (Table 3), suhB is a super-regulator involved in the proper rRNA folding (Singh et al, 2016). It plays a role in virulence of animal bacterial pathogens, influencing T3SS, T6SS, flagellum and biofilm regulation and probably acts in opposite ways in different bacteria (Rosales-Reyes et al, 2012; Li et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii

et al. 2017

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Bacterial wilt of potatoes—also called brown rot—is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.

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“…The N-terminal domain (NTD or NGN) anchors NusG to the clamp helices of the RNAP β’ subunit, whereas the C-terminal domain (CTD or KOW) interacts with the components of the downstream processes (reviewed in [Belogurov and Artsimovitch, 2015]). In E. coli , NusG CTD interacts with NusE as part of the ribosome on protein coding operons (Burmann et al, 2010) or as a part of a so-called antitermination complex (NusABEG) on ribosomal RNA operons (Zellars and Squires, 1999; Shankar et al, 2007; Singh et al, 2016); in these contexts, NusG inhibits the function of a transcription termination factor Rho. If neither ribosome nor antitermination complex is engaged, which often implies that transcription is futile, NusG CTD binds to Rho and facilitates termination of transcription (Cardinale et al, 2008; Peters et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

Turtola

Belogurov

2016

eLife

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Universally conserved factors from NusG family bind at the upstream fork junction of transcription elongation complexes and modulate RNA synthesis in response to translation, processing, and folding of the nascent RNA. Escherichia coli NusG enhances transcription elongation in vitro by a poorly understood mechanism. Here we report that E. coli NusG slows Gre factor-stimulated cleavage of the nascent RNA, but does not measurably change the rates of single nucleotide addition and translocation by a non-paused RNA polymerase. We demonstrate that NusG slows RNA cleavage by inhibiting backtracking. This activity is abolished by mismatches in the upstream DNA and is independent of the gate and rudder loops, but is partially dependent on the lid loop. Our comprehensive mapping of the upstream fork junction by base analogue fluorescence and nucleic acids crosslinking suggests that NusG inhibits backtracking by stabilizing the minimal transcription bubble.DOI: http://dx.doi.org/10.7554/eLife.18096.001

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SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli

Cited by 43 publications

References 63 publications

A Screen for rfaH Suppressors Reveals a Key Role for a Connector Region of Termination Factor Rho

A Screen for rfaH Suppressors Reveals a Key Role for a Connector Region of Termination Factor Rho

Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

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