Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans -Translation
Authors: Sathish Kumar
Nawsad Alam
Ora Schueler-Furman
Hanna Engelberg-Kulka
Oliver Vesper
Isabella Moll
Ilana Kolodkin-Gal
Journal: mBio (2016)
Discipline: MICROBIOLOGY
Keywords: Escherichia coli; mazEF; stress-induced; toxin-antitoxin module; cell death
Affiliations: Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel., Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel., Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria., Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel .

Abstract:  Eshcerichia coli mazEF is a stress-induced toxin-antitoxin module mediating cell death and requiring a quorum-sensing (QS) extracellular death factor (EDF), the pentapeptide NNWNN. Here we uncovered several distinct molecular mechanisms involved in its generation from the zwf mRNA encoding glucose-6-phosphate dehydrogenase. In particular, we show that, under stress conditions, the endoribonuclease MazF cleaves specific ACA sites, thereby generating a leaderless zwf mRNA which is truncated 30 codons after the EDF-encoding region. Since the nascent ribosome peptide exit tunnel can accommodate up to 40 amino acids, this arrangement allows the localization of the EDF residues inside the tunnel when the ribosome is stalled at the truncation site. Moreover, ribosome stalling activates the trans-translation system, which provides a means for the involvement of ClpPX in EDF generation. Furthermore, the trans-translation is described as a regulatory system that attenuated the generation of EDF, leading to low levels of EDF in the single cell. Therefore, the threshold EDF molecule concentration required is achieved only by the whole population, as expected for QS. Importance: Bacteria communicate with one another via quorum-sensing (QS) signal molecules. QS provides a mechanism for bacteria to monitor each other's presence and to modulate gene expression in response to population density. Previously, we added E. coli pentapeptide EDF to this list of QS molecules. We showed that, under stress conditions, the induced MazF, an endoribonuclease cleaving at ACA sites, generates EDF from zwf. Here we studied the mechanism of EDF generation and asked whether it is related to EDF density dependency. We illustrated that, under stress conditions, multiple distinct complex mechanisms are involved in EDF generation. This includes formation of leaderless truncated zwf mRNA by MazF, configuration of a length corresponding to the nascent ribosome peptide exit tunnel, rescue performed by the trans-translation system, and cleavage by ClpPX protease. trans-Translation is described as a regulatory system attenuating EDF generation and leading to low levels of EDF in the single cell, as expected for QS. 

Retracted: No

PubPeer comments:
 The study is described as a prospective research in humans and performed in France: * the purpose of the present study was to determine whether the increase in glycolytic metabolism during growth, assessed by AODgly and blood metabolic responses (i.e. increased blood lactate accumulation and decreased pH) is principally infuenced by concomitant changes in LBM.  * This study included minors: * Thirty-six male competitive rowers aged from 11 to 17 years volunteered to participate in the present study * The study has been performed on healthy volunteers, medical parameters were collected and interventions using a device were done : * Volunteers were tested in two experimental sessions separated by at least 48 h. Participants were instructed not to undertake any strenuous activity during the 24 h preceding each session. The frst session was dedicated to gathering participantsu2019 physical characteristics (anthropometric measurements, body composition and maturity status) and maximal oxygen uptake (VOu0307 2max) assessment. During the second session, the volunteers performed a 60-s all-out test. * As a consequence, It is definitely a prospective research in human (RIPH) with regards of the french law. According the [SmartReg Tool from the Girci] , the anthropometric measurement is sufficient to define this study as an RIPH. There is few hesitation here on the definition of this study as a RIPH. In France, all RIPHs (whatever the level) require the approval from a CPP before to start the recruitment of participants. Starting a prospective research in humans in France without a CPP is a serious breach to the Health French Law. Especially when minors are included in the study. The ethic statement of this study is described as follows: * The present study was approved by an institutional ethics review board (Comitu00e9 du2019u00c9thique pour la Recherche en Sciences et Techniques des Activitu00e9s Physiques et Sportivesu2014CERSTAPS, nu00b0 2017-29-11-20) and conformed to the standards of use of human participants in research as outlined in the Sixth Declaration of Helsinki. The participants were informed of the experimental procedures and gave their written assent before any testing was conducted. In addition, the written informed consent was obtained from the parents or legal guardians of the participants. * The CERSTAPS is not a Comitu00e9 de Protection des Personnes (CPP). As mentioned on the [CERSTAPS website] itself, a prospective research in humans in France MUST obtain an approval from a CPP before to start. The ethics statement do not provide any information related to a CPP approval. Can the authors clarify: - If they obtain a CPP approval before to start the recruitment? - If they request a CPP approval? In this case, what was the answer of the CPP ? If a CPP provides a waiver for the approval, the article should mention it and detail the waiver in order to raise any question on ethics procedure. However, if the CPP approval or a waiver from a CPP has not been obtained, this is a major infringement to the Health French Law and the Declaration of Helsinki (article 23). If the study is in this situation, it may be a serious ethical issue. ,