Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates Lydia Hadjeras, Marie Bouvier, Isabelle Canal, Leonora Poljak, Quentin Morin-Ogier, Carine Froment, Odile Burlet-Schlitz, Lina Hamouche, Laurence Girbal, Muriel Cocaign-Bousquet, Agamemnon J. Carpousis Plos Biology, 2023 RNA processing and degradation shape the transcriptome by generating stable molecules that are necessary for translation (rRNA and tRNA) and by facilitating the turnover of mRNA, which is necessary for the posttranscriptional control of gene expression. In bacteria and the plant chloroplast, RNA degradosomes are multienzyme complexes that process and degrade RNA. In many bacterial species, the endoribonuclease RNase E is the central component of the RNA degradosome. RNase E-based RNA degradosomes are inner membrane proteins in a large family of gram-negative bacteria (β- and γ-Proteobacteria). Until now, the reason for membrane localization was not understood. Here, we show that a mutant strain ofEscherichia coli, in which the RNA degradosome is localized to the interior of the cell, has high levels of 20S and 40S particles that are defective intermediates in ribosome assembly. These particles have aberrant protein composition and contain rRNA precursors that have been cleaved by RNase E. After RNase E cleavage, rRNA fragments are degraded to nucleotides by exoribonucleases. In vitro, rRNA in intact ribosomes is resistant to RNase E cleavage, whereas protein-free rRNA is readily degraded. We conclude that RNA degradosomes in the nucleoid of the mutant strain interfere with cotranscriptional ribosome assembly. We propose that membrane-attached RNA degradosomes in wild-type cells control the quality of ribosome assembly after intermediates are released from the nucleoid. That is, the compact structure of mature ribosomes protects rRNA against cleavage by RNase E. Turnover of a proportion of intermediates in ribosome assembly explains slow growth of the mutant strain. Competition between mRNA and rRNA degradation could be the cause of slower mRNA degradation in the mutant strain. We conclude that attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA precursors, thus explaining the reason for conservation of membrane-attached RNA degradosomes throughout the β- and γ-Proteobacteria.
Compartmentalization of RNA Degradosomes in Bacteria Controls Accessibility to Substrates and Ensures Concerted Degradation of mRNA to Nucleotides Agamemnon J. Carpousis, Nathalie Campo, Lydia Hadjeras, Lina Hamouche Annual Review of Microbiology, 2022 RNA degradosomes are multienzyme complexes composed of ribonucleases, RNA helicases, and metabolic enzymes. RNase E–based degradosomes are widespread in Proteobacteria. The Escherichia coli RNA degradosome is sequestered from transcription in the nucleoid and translation in the cytoplasm by localization to the inner cytoplasmic membrane, where it forms short-lived clusters that are proposed to be sites of mRNA degradation. In Caulobacter crescentus, RNA degradosomes localize to ribonucleoprotein condensates in the interior of the cell [bacterial ribonucleoprotein-bodies (BR-bodies)], which have been proposed to drive the concerted degradation of mRNA to nucleotides. The turnover of mRNA in growing cells is important for maintaining pools of nucleotides for transcription and DNA replication.Membrane attachment of the E. coli RNA degradosome is necessary to avoid wasteful degradation of intermediates in ribosome assembly. Sequestering RNA degradosomes to C. crescentus BR-bodies, which exclude structured RNA, could have a similar role in protecting intermediates in ribosome assembly from degradation.
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin Lina Hamouche, Leonora Poljak, Agamemnon J. Carpousis RNA, 2021 Rifampicin, a broad-spectrum antibiotic, inhibits bacterial RNA polymerase. Here we show that rifampicin treatment ofEscherichia coliresults in a 50% decrease in cell size due to a terminal cell division. This decrease is a consequence of inhibition of transcription as evidenced by an isogenic rifampicin-resistant strain. There is also a 50% decrease in total RNA due mostly to a 90% decrease in 23S and 16S rRNA levels. Control experiments showed this decrease is not an artifact of our RNA purification protocol and therefore due to degradation in vivo. Since chromosome replication continues after rifampicin treatment, ribonucleotides from rRNA degradation could be recycled for DNA synthesis. Rifampicin-induced rRNA degradation occurs under different growth conditions and in different strain backgrounds. However, rRNA degradation is never complete, thus permitting the reinitiation of growth after removal of rifampicin. The orderly shutdown of growth under conditions where the induction of stress genes is blocked by rifampicin is noteworthy. Inhibition of protein synthesis by chloramphenicol resulted in a partial decrease in 23S and 16S rRNA levels whereas kasugamycin treatment had no effect. Analysis of temperature-sensitive mutant strains implicate RNase E, PNPase, and RNase R in rifampicin-induced rRNA degradation. We cannot distinguish between a direct role for RNase E in rRNA degradation versus an indirect role involving a slowdown of mRNA degradation. Since mRNA and rRNA appear to be degraded by the same ribonucleases, competition by rRNA is likely to result in slower mRNA degradation rates in the presence of rifampicin than under normal growth conditions.
Dynamic membrane localization of RNase Y in bacillus subtilis Lina Hamouche, Cyrille Billaudeau, Anna Rocca, Arnaud Chastanet, Saravuth Ngo, Soumaya Laalami, Harald Putzer Mbio, 2020 All living organisms must degrade mRNA to adapt gene expression to changing environments. In bacteria, initiation of mRNA decay generally occurs through an endonucleolytic cleavage. In the Gram-positive model organism Bacillus subtilis and probably many other bacteria, the key enzyme for this task is RNase Y, which is anchored at the inner cell membrane. While this pseudocompartmentalization appears coherent with translation occurring primarily at the cell periphery, our knowledge on the distribution and dynamics of RNase Y in living cells is very scarce. Here, we show that RNase Y moves rapidly along the membrane in the form of dynamic short-lived foci. These foci become more abundant and increase in size following transcription arrest, suggesting that they do not constitute the most active form of the nuclease. This contrasts with RNase E, the major decay-initiating RNase in E. coli , where it was shown that formation of foci is dependent on the presence of RNA substrates. We also show that a protein complex (Y-complex) known to influence the specificity of RNase Y activity in vivo is capable of shifting the assembly status of RNase Y toward fewer and smaller complexes. This highlights fundamental differences between RNase E- and RNase Y-based degradation machineries.
Bacillus subtilis swarmer cells lead the swarm, multiply, and generate a trail of quiescent descendants Lina Hamouche, Soumaya Laalami, Adrian Daerr, Solène Song, I. Barry Holland, Simone J. Séror, Kassem Hamze, Harald Putzer Mbio, 2017 Bacteria adopt social behavior to expand into new territory, led by specialized swarmers, before forming a biofilm. Such mass migration of Bacillus subtilis on a synthetic medium produces hyperbranching dendrites that transiently (equivalent to 4 to 5 generations of growth) maintain a cellular monolayer over long distances, greatly facilitating single-cell gene expression analysis. Paradoxically, while cells in the dendrites (nonswarmers) might be expected to grow exponentially, the rate of swarm expansion is constant, suggesting that some cells are not multiplying. Little attention has been paid to which cells in a swarm are actually multiplying and contributing to the overall biomass. Here, we show in situ that DNA replication, protein translation and peptidoglycan synthesis are primarily restricted to the swarmer cells at dendrite tips. Thus, these specialized cells not only lead the population forward but are apparently the source of all cells in the stems of early dendrites. We developed a simple mathematical model that supports this conclusion. IMPORTANCE Swarming motility enables rapid coordinated surface translocation of a microbial community, preceding the formation of a biofilm. This movement occurs in thin films and involves specialized swarmer cells localized to a narrow zone at the extreme swarm edge. In the B. subtilis system, using a synthetic medium, the swarm front remains as a cellular monolayer for up to 1.5 cm. Swarmers display high-velocity whirls and vortexing and are often assumed to drive community expansion at the expense of cell growth. Surprisingly, little attention has been paid to which cells in a swarm are actually growing and contributing to the overall biomass. Here, we show that swarmers not only lead the population forward but continue to multiply as a source of all cells in the community. We present a model that explains how exponential growth of only a few cells is compatible with the linear expansion rate of the swarm.
RECENT SCHOLAR PUBLICATIONS
Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates L Hadjeras, M Bouvier, I Canal, L Poljak, Q Morin-Ogier, C Froment, ... PLoS Biology 21 (1), e3001942 , 2023 2023 Citations: 8
Compartmentalization of RNA degradosomes in bacteria controls accessibility to substrates and ensures concerted degradation of mRNA to nucleotides AJ Carpousis, N Campo, L Hadjeras, L Hamouche Annual Review of Microbiology 76, 533-552 , 2022 2022 Citations: 22
Attachment of the RNA degradosome to the inner cytoplasmic membrane of Escherichia coli prevents wasteful degradation of rRNA intermediates in ribosome … L Hadjeras, M Bouvier, I Canal, L Poljak, Q Morin-Ogier, C Froment, ... bioRxiv, 2022.06. 14.496040 , 2022 2022
Ribosome quality control in Escherichia coli requires attachment of the RNA degradosome to the inner cytoplasmic membrane to prevent wasteful degradation of intermediates in … A Carpousis, L Hadjeras, M Bouvier, I Canal, L Poljak, Q Morin-Ogier, ... 2022
Agamemnon J. Carpousis, Nathalie Campo L Hadjeras, L Hamouche Annu. Rev. Microbiol 76, 533-52 , 2022 2022
Dynamics of RNase Y in B. subtilis: cytoplasmic pattern of localization revisited L Hamouche, H Putzer Nucleic Acids Research , 2021 2021
Polyribosome-Dependent Clustering of Membrane-Anchored RNA Degradosomes To Form Sites of mRNA Degradation in Escherichia coli L Hamouche, L Poljak, AJ Carpousis mBio journal 12 (5), e01932-21 , 2021 2021 Citations: 15
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin L Hamouche, L Poljak, AJ Carpousis RNA journal , 2021 2021 Citations: 42
Dynamic Membrane Localization of RNase Y in Bacillus subtilis L Hamouche, C Billaudeau, A Rocca, A Chastanet, S Ngo, S Laalami, ... mBio 11 (1), 03337-19 , 2020 2020 Citations: 42
Dynamic membrane localization of RNase Y in Bacillus subtilis. mBio 11: e03337-19 L Hamouche, C Billaudeau, A Rocca, A Chastanet, S Ngo, S Laalami, ... Crossref, Medline , 2020 2020 Citations: 10
Bacillus subtilis swarmer cells lead the swarm, multiply, and generate a trail of quiescent descendants L Hamouche, S Laalami, A Daerr, S Song, IB Holland, SJ Séror, K Hamze, ... mBio 8 (1), e02102-16 , 2017 2017 Citations: 23
Bacillus subtilis swarmer cells lead the swarm, multiply, and generate a trail of quiescent descendants. mBio 8: e02102-16 L Hamouche, S Laalami, A Daerr, S Song, IB Holland, SJ Séror, K Hamze, ... 2017 Citations: 5
The Effect Of Chemotaxis On The Swarming Ability Of Bacillus subtilis: Critical Effect Of Glutamic Acid And Lysine L Hamouche, S Laalami, G Lakkis, A Kobaissi, A Chokr, H Putzer, ... 2015 Citations: 1
Contrôle spatio-temporel de l'expression génétique et du comportement d'une communauté migrante de Bacillus subtilis L Hamouche University Sorbonne Paris Cité, Paris Diderot , 2015 2015
MOST CITED SCHOLAR PUBLICATIONS
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin L Hamouche, L Poljak, AJ Carpousis RNA journal , 2021 2021 Citations: 42
Dynamic Membrane Localization of RNase Y in Bacillus subtilis L Hamouche, C Billaudeau, A Rocca, A Chastanet, S Ngo, S Laalami, ... mBio 11 (1), 03337-19 , 2020 2020 Citations: 42
Bacillus subtilis swarmer cells lead the swarm, multiply, and generate a trail of quiescent descendants L Hamouche, S Laalami, A Daerr, S Song, IB Holland, SJ Séror, K Hamze, ... mBio 8 (1), e02102-16 , 2017 2017 Citations: 23
Compartmentalization of RNA degradosomes in bacteria controls accessibility to substrates and ensures concerted degradation of mRNA to nucleotides AJ Carpousis, N Campo, L Hadjeras, L Hamouche Annual Review of Microbiology 76, 533-552 , 2022 2022 Citations: 22
Polyribosome-Dependent Clustering of Membrane-Anchored RNA Degradosomes To Form Sites of mRNA Degradation in Escherichia coli L Hamouche, L Poljak, AJ Carpousis mBio journal 12 (5), e01932-21 , 2021 2021 Citations: 15
Dynamic membrane localization of RNase Y in Bacillus subtilis. mBio 11: e03337-19 L Hamouche, C Billaudeau, A Rocca, A Chastanet, S Ngo, S Laalami, ... Crossref, Medline , 2020 2020 Citations: 10
Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates L Hadjeras, M Bouvier, I Canal, L Poljak, Q Morin-Ogier, C Froment, ... PLoS Biology 21 (1), e3001942 , 2023 2023 Citations: 8
Bacillus subtilis swarmer cells lead the swarm, multiply, and generate a trail of quiescent descendants. mBio 8: e02102-16 L Hamouche, S Laalami, A Daerr, S Song, IB Holland, SJ Séror, K Hamze, ... 2017 Citations: 5
The Effect Of Chemotaxis On The Swarming Ability Of Bacillus subtilis: Critical Effect Of Glutamic Acid And Lysine L Hamouche, S Laalami, G Lakkis, A Kobaissi, A Chokr, H Putzer, ... 2015 Citations: 1
Attachment of the RNA degradosome to the inner cytoplasmic membrane of Escherichia coli prevents wasteful degradation of rRNA intermediates in ribosome … L Hadjeras, M Bouvier, I Canal, L Poljak, Q Morin-Ogier, C Froment, ... bioRxiv, 2022.06. 14.496040 , 2022 2022
Ribosome quality control in Escherichia coli requires attachment of the RNA degradosome to the inner cytoplasmic membrane to prevent wasteful degradation of intermediates in … A Carpousis, L Hadjeras, M Bouvier, I Canal, L Poljak, Q Morin-Ogier, ... 2022
Agamemnon J. Carpousis, Nathalie Campo L Hadjeras, L Hamouche Annu. Rev. Microbiol 76, 533-52 , 2022 2022
Dynamics of RNase Y in B. subtilis: cytoplasmic pattern of localization revisited L Hamouche, H Putzer Nucleic Acids Research , 2021 2021
Contrôle spatio-temporel de l'expression génétique et du comportement d'une communauté migrante de Bacillus subtilis L Hamouche University Sorbonne Paris Cité, Paris Diderot , 2015 2015
