Regulation of the macrolide resistance ABC-F translation factor MsrD

Fostier, Corentin R.; Ousalem, Farès; Leroy, Elodie C.; Ngo, Saravuth; Soufari, Heddy; Innis, C.A.; Hashem, Yaser; Boël, Grégory

doi:10.1101/2021.11.29.470318

Cited by 4 publications

(7 citation statements)

References 108 publications

(286 reference statements)

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“…Collectively, our results suggest that the regulatory mechanism controlling VmlR expression is analogous (although probably not homologous) to that described for Streptococcal MsrD macrolide ABCF resistance factor ( 73 ). Similar to VmlR, induction of MsrD requires antibiotic-specific (macrolide-specific elongation arrest in this case) ribosomal stalling on the uORF to counter constitutive intrinsic transcription termination.…”

Section: Resultssupporting

confidence: 51%

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Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp

Takada

Mandell

Yakhnin

et al. 2022

Nucleic Acids Research

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Since antibiotic resistance is often associated with a fitness cost, bacteria employ multi-layered regulatory mechanisms to ensure that expression of resistance factors is restricted to times of antibiotic challenge. In Bacillus subtilis, the chromosomally-encoded ABCF ATPase VmlR confers resistance to pleuromutilin, lincosamide and type A streptogramin translation inhibitors. Here we show that vmlR expression is regulated by translation attenuation and transcription attenuation mechanisms. Antibiotic-induced ribosome stalling during translation of an upstream open reading frame in the vmlR leader region prevents formation of an anti-antiterminator structure, leading to the formation of an antiterminator structure that prevents intrinsic termination. Thus, transcription in the presence of antibiotic induces vmlR expression. We also show that NusG-dependent RNA polymerase pausing in the vmlR leader prevents leaky expression in the absence of antibiotic. Furthermore, we demonstrate that induction of VmlR expression by compromised protein synthesis does not require the ability of VmlR to rescue the translational defect, as exemplified by constitutive induction of VmlR by ribosome assembly defects. Rather, the specificity of induction is determined by the antibiotic's ability to stall the ribosome on the regulatory open reading frame located within the vmlR leader. Finally, we demonstrate the involvement of (p)ppGpp-mediated signalling in antibiotic-induced VmlR expression.

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Section: Resultssupporting

confidence: 51%

“…Similar to VmlR, induction of MsrD requires antibiotic-specific (macrolide-specific elongation arrest in this case) ribosomal stalling on the uORF to counter constitutive intrinsic transcription termination. Unlike the case with VmlR, a NusG-dependent pause site was not identified in the msrD mRNA 5′ region ( 73 ).…”

Section: Resultsmentioning

confidence: 99%

Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp

Takada

Mandell

Yakhnin

et al. 2022

Nucleic Acids Research

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“…S4C ). Further study is required to fully understand the physiological significance of YheS and other ABCFs in gene expression regulation as ARE-ABCFs (25, 45, 46).…”

Section: Discussionmentioning

confidence: 99%

“…S4C). Further study is required to fully understand the physiological significance of YheS and other ABCFs in gene expression regulation as ARE-ABCFs (25,45,46). The limited impact of ABCFs on distinct noncanonical translations suggests that each ABCF may have specialized interactions with certain structural elements or sequences of translating ribosomes.…”

Section: Discussionmentioning

confidence: 99%

The ABCF proteins inEscherichia coliindividually alleviate nascent peptide-induced noncanonical translations

Chadani,

Uemura,

Yamazaki

et al. 2023

Preprint

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Organisms possess a wide variety of proteins with a diverse repertoire of amino acid sequences, and their synthesis relies on the ribosome. Empirical observations have led to the misconception that ribosomes are robust protein factories, but in reality, they have several weaknesses. For instance, ribosomes stall during the translation of the proline-rich sequences, but the translation elongation factor EF-P assists in synthesizing proteins containing the poly-proline sequences. Thus, living organisms have evolved to expand the translation capability of ribosomes through the acquisition of translation elongation factors, enabling the synthesis of diverse proteins.In this study, we have revealed thatEscherichia coliATP-Binding Cassette family-F (ABCF) proteins, YheS, YbiT, EttA and Uup, individually cope with various noncanonical translations induced by nascent peptide sequences within the exit tunnel of the ribosome. The correspondence between noncanonical translations and ABCFs was YheS for the translational arrest by nascent SecM, YbiT for poly-basic sequence-dependent ribosome stalling and poly-acidic sequence-dependent intrinsic ribosome destabilization (IRD), EttA for IRD at the early stage of elongation, and Uup for poly-proline-dependent stalling. Our results suggest that the ATP hydrolysis-coupled structural rearrangement and interdomain linker sequence between the two nucleotide-binding domains play crucial roles in alleviating the noncanonical translations. Our study highlights a new aspect of ABCF proteins to reduce the potential risks that are encoded within the nascent peptide sequences.Significance statementProteins, that constitute living organisms, exhibit a diverse range of amino acid sequences. However, it has become evident that ribosomes have difficulties in synthesizing certain amino acid sequences, including the poly-basic, poly-acidic, and poly-proline sequences. The mechanisms underlying the expression of proteins with such challenging sequences remain largely elusive. In this study, we have unveiled that translation factor ABCF proteins inEscherichia colipromote various kinds of problematic amino acid sequences that inhibit efficient translation. Through the actions of translation elongation factors including the ABCF proteins, the translation system acquires robustness in synthesizing a vast repertoire of amino acid sequences.

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“…With the EF-P/eIF-5A protein that has been identified to rescue ribosomes stalled during the synthesis of polyproline-containing proteins [24][25][26] , ABC-F are the only factors known to bind to the ribosomal E site. Some ABC-F have a clear physiological function such as the antibiotic resistance ABC-F (ARE ABC-F) factors 4,5,7,[9][10][11][12][13][14][15]27,28 which provide resistance toward antibiotics that target the PTC and the nascent peptide exit tunnel (NPET) of the ribosome 4,5,7,11,12,14,15 . However, for most of the family, their physiological function remains unclear.…”

Section: Mainmentioning

confidence: 99%

Global regulation via modulation of ribosome pausing by the ABC-F protein EttA

Ousalem,

Ngo,

Oïffer

et al. 2023

Preprint

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Having multiple rounds of translation of the same mRNA is a key feature of the Central Dogma that creates substantial dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences. The molecular mechanisms controlling these critical processes and the principles guiding their evolution remain among the least understood facets of cellular physiology. We herein use a combination of genetic, genomic, physiological, and biochemical methods to show that regulation of ribosome pausing at specific amino acid sequences can produce ~2-fold changes in protein expression levels that have a strong influence on cell growth and therefore evolutionary fitness. We demonstrate, both in vivo and in vitro, that the ABCF protein EttA directly controls the translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle and its glyoxylate shunt, which dramatically modulates growth in some chemical environments. It also modulates expression of specific proteins involved in metabolically related physiological and stress-response pathways. These regulatory activities are mediated by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within the first 30 amino acids of nascent proteins. The previously established dependency of EttA's activity on ADP:ATP ratio can modulate these effects based on cellular energy status. We thus establish a new global regulatory paradigm based on sequence-specific modulation of translational pausing.

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Regulation of the macrolide resistance ABC-F translation factor MsrD

Cited by 4 publications

References 108 publications

Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp

Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp

The ABCF proteins inEscherichia coliindividually alleviate nascent peptide-induced noncanonical translations

Global regulation via modulation of ribosome pausing by the ABC-F protein EttA

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