The Structural Basis for mRNA Recognition and Cleavage by the Ribosome-Dependent Endonuclease RelE

Neubauer, Cajetan; Gao, Yong‐Gui; Andersen, Kasper R.; Dunham, C.M.; Kelley, A.C.; Hentschel, Jendrik; Gerdes, Kenn; Ramakrishnan, V.; Brodersen, D.E.

doi:10.1016/j.cell.2009.11.015

Cited by 197 publications

(369 citation statements)

References 45 publications

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“…On the other hand, these observations, of course, do not exclude that particular TA loci have been recruited to perform other functions, as recently proposed for the mqsRA locus of E. coli (47). The entirely different tertiary folds of the translational inhibitors encoded by type II TA loci, such as RelE, MazF, and HicA, indicate that they have independent evolutionary origins (7,15,(48)(49)(50)(51). Therefore, the common genetic organization, transcriptional regulation, and cellular targets (i.e., translation) of type II TA loci suggest that these gene families emerged by convergent evolution.…”

Section: Discussionmentioning

confidence: 86%

“…RelE of E. coli belongs to a well-described toxin superfamily with many homologs in both bacteria and archaea (13). RelE is a riboendonuclease that cleaves mRNA positioned at the ribosomal A site, between the second and third bases of the A-site codon (14,15). Therefore, ectopic production of RelE rapidly shuts down translation and halts cell growth (16).…”

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confidence: 99%

“…In all cases, ectopic production of the mRNases leads to a rapid degradation of mRNA and shut-down of translation (14,(19)(20)(21). Six of the mRNases (RelE, YoeB, HigB, YhaV, YafO, and YafQ) cleave mRNA positioned at the ribosomal A site (14,15,(21)(22)(23)(24), whereas the other 4 (MazF, ChpB, MqsR, and HicA) cleave RNA sitespecifically, independent of the ribosomes (19,20,25). The 10 mRNases and their cognate antitoxins are encoded by bicistronic operons that are autoregulated by the antitoxins, which bind to operator sequences in the TA promoter regions (10).…”

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confidence: 99%

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RETRACTED: Bacterial persistence by RNA endonucleases

Maisonneuve

Shakespeare

Jørgensen

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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557

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Bacteria form persisters, individual cells that are highly tolerant to different types of antibiotics. Persister cells are genetically identical to nontolerant kin but have entered a dormant state in which they are recalcitrant to the killing activity of the antibiotics. The molecular mechanisms underlying bacterial persistence are unknown. Here, we show that the ubiquitous Lon (Long Form Filament) protease and mRNA endonucleases (mRNases) encoded by toxin-antitoxin (TA) loci are required for persistence in Escherichia coli . Successive deletion of the 10 mRNase-encoding TA loci of E . coli progressively reduced the level of persisters, showing that persistence is a phenotype common to TA loci. In all cases tested, the antitoxins, which control the activities of the mRNases, are Lon substrates. Consistently, cells lacking lon generated a highly reduced level of persisters. Moreover, Lon overproduction dramatically increased the levels of persisters in wild-type cells but not in cells lacking the 10 mRNases. These results support a simple model according to which mRNases encoded by TA loci are activated in a small fraction of growing cells by Lon-mediated degradation of the antitoxins. Activation of the mRNases, in turn, inhibits global cellular translation, and thereby induces dormancy and persistence. Many pathogenic bacteria known to enter dormant states have a plethora of TA genes. Therefore, in the future, the discoveries described here may lead to a mechanistic understanding of the persistence phenomenon in pathogenic bacteria.

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Section: Discussionmentioning

confidence: 86%

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confidence: 99%

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confidence: 99%

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RETRACTED: Bacterial persistence by RNA endonucleases

Maisonneuve

Shakespeare

Jørgensen

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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459

557

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“…Ribosome-dependent toxins cleave mRNAs on the ribosome between the second and third nucleotides of the aminoacyl (A)-site codon (21)(22)(23). Although collectively Escherichia coli ribosome-dependent toxins target a diverse range of codons, each individual toxin appears to have a strong codon preference and cleaves at defined positions along the mRNA (24)(25)(26).…”

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confidence: 99%

Defining the mRNA recognition signature of a bacterial toxin protein

Schureck

Dunkle

Maehigashi

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosomedependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. Here, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop to recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide. (1,3,4). This rapid inhibitory switch suppresses metabolite consumption and temporarily halts cell growth to promote bacterial survival until nutrients are readily available. Among the prosurvival genes regulated by (p)ppGpp production are toxin-antitoxin modules, which have additional roles in antibiotic resistance and tolerance, biofilm and persister cell formation, and niche-specific colonization (5-11). The critical roles toxin-antitoxin pairs play in bacterial physiology underscore the importance of understanding their molecular targets and modes of action.There are five different classes (I to V) of toxin-antitoxin systems defined by how the antitoxin represses toxin function (1). Type II toxin-antitoxin pairs form protein-protein complexes during exponential growth that serve two purposes: inhibition of toxin activity by antitoxin binding and transcriptional autorepression to limit toxin expression (12). Antitoxins are proteolytically degraded after (p)ppGpp accumulation, leading to derepression at the toxin-antitoxin promoter (8, 12). Liberated toxin proteins inhibit the replication or translation machinery by targeting DNA gyrase, initiator tRNA fMet , glutamyl-tRNA synthetase, EF-Tu, free mRNA, ribosome-bound mRNA, and the ribosome itself (13-20).Ribosome-dependent toxins cleave mRNAs on the ribosome between the second and third nucleotides of the aminoacyl (A)-site codon (21-23). Although collectively Escherichia coli ribosome-dependent toxins target a diverse range of codons, each individual toxin appears to have a strong codon preference and cleaves at defined positions along the mRNA (24-26). RelE cleaves at UAG stop codons and the CAG sense codon (all codons denoted in the 5′-3′ direction); YoeB cleaves at codons following a translational AUG start site and at the UAA stop codon; and YafQ cleaves a single AAA sense codon (16,24,(27)(28)(29). In contrast, Proteus vulgaris host inhibition of growth B (HigB) toxin degrades multiple codons encod...

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“…A few years later the first two chromosome-encoded type II TA loci, homologues of pemIK (also called mazEF), were identified [23]. We discovered the relBE module of E. coli (figure 1a) and showed that relE encodes an efficient inhibitor of global cellular translation [28,31] that cleaves mRNA codons at the ribosomal A-site [25,26]. Over the years, we have developed relBE of E. coli into a paradigm model system, not least because relBE homologues are abundantly present in bacterial and archaeal chromosomes [17].…”

Section: Introductionmentioning

confidence: 99%

Hypothesis: type I toxin–antitoxin genes enter the persistence field—a feedback mechanism explaining membrane homoeostasis

Gerdes

2016

Phil. Trans. R. Soc. B

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Bacteria form persisters, cells that are tolerant to multiple antibiotics and other types of environmental stress. Persister formation can be induced either stochastically in single cells of a growing bacterial ensemble, or by environmental stresses, such as nutrient starvation, in a subpopulation of cells. In many cases, the molecular mechanisms underlying persistence are still unknown. However, there is growing evidence that, in enterobacteria, both stochastically and environmentally induced persistence are controlled by the second messenger (p)ppGpp. For example, the ‘alarmone’ (p)ppGpp activates Lon, which, in turn, activates type II toxin–antitoxin (TA) modules to thereby induce persistence. Recently, it has been shown that a type I TA module, hokB / sokB , also can induce persistence. In this case, the underlying mechanism depends on the universally conserved GTPase Obg and, surprisingly, also (p)ppGpp. In the presence of (p)ppGpp, Obg stimulates hokB transcription and induces persistence. HokB toxin expression is under both negative and positive control: SokB antisense RNA inhibits hokB mRNA translation, while (p)ppGpp and Obg together stimulate hokB transcription. HokB is a small toxic membrane protein that, when produced in modest amounts, leads to membrane depolarization, cell stasis and persistence. By contrast, overexpression of HokB disrupts the membrane potential and kills the cell. These observations raise the question of how expression of HokB is regulated. Here, I propose a homoeostatic control mechanism that couples HokB expression to the membrane-bound RNase E that degrades and inactivates SokB antisense RNA. This article is part of the themed issue ‘The new bacteriology’.

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The Structural Basis for mRNA Recognition and Cleavage by the Ribosome-Dependent Endonuclease RelE

Cited by 197 publications

References 45 publications

RETRACTED: Bacterial persistence by RNA endonucleases

RETRACTED: Bacterial persistence by RNA endonucleases

Defining the mRNA recognition signature of a bacterial toxin protein

Hypothesis: type I toxin–antitoxin genes enter the persistence field—a feedback mechanism explaining membrane homoeostasis

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